ORCID Profile
0000-0002-1285-7947
Current Organisations
Brighton and Sussex Medical School
,
University of Plymouth
,
Walter and Eliza Hall Institute of Medical Research
,
University of Melbourne
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Microbiology | Genetics | Veterinary Sciences | Infectious Agents | Gene Expression (incl. Microarray and other genome-wide approaches) | Microbial Ecology | Genomics | Other Biological Sciences | Genome Structure | Population And Ecological Genetics | Biological Sciences not elsewhere classified | Water Quality Engineering | Civil Engineering | Systems Biology | Microbiology not elsewhere classified | Parasitology | Proteomics and Intermolecular Interactions (excl. Medical Proteomics) | Veterinary Parasitology | Veterinary Immunology | Public Health And Health Services Not Elsewhere Classified | Infectious Agents | Molecular Evolution | Infectious Diseases | Natural Resource Management | Biological Adaptation
ANZSRC Socio-Economic Objective (SEO)
Infectious diseases | Biological sciences | Expanding Knowledge in the Biological Sciences | Urban Water Evaluation (incl. Water Quality) | Infectious Diseases | Control of Animal Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Control of pests and exotic species | Expanding Knowledge in the Medical and Health Sciences | Water Recycling Services (incl. Sewage and Greywater) | Urban and Industrial Water Management | Sheep - Meat | Physical and Chemical Conditions of Water in Fresh, Ground and Surface Water Environments (excl. Urban and Industrial Use) | Sheep - Wool | Zoonoses | Water services and utilities | Rural Water Evaluation (incl. Water Quality) |
Related Links
Publications
Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures
Publisher: Public Library of Science (PLoS)
Date: 04-08-2022
DOI: 10.1371/JOURNAL.PNTD.0010633
Abstract: Plasmodium vivax sporozoites reside in the salivary glands of a mosquito before infecting a human host and causing malaria. Previous transcriptome-wide studies in populations of these parasite forms were limited in their ability to elucidate cell-to-cell variation, thereby masking cellular states potentially important in understanding malaria transmission outcomes. In this study, we performed transcription profiling on 9,947 P . vivax sporozoites to assess the extent to which they differ at single-cell resolution. We show that sporozoites residing in the mosquito’s salivary glands exist in distinct developmental states, as defined by their transcriptomic signatures. Additionally, relative to P . falciparum , P . vivax displays overlapping and unique gene usage patterns, highlighting conserved and species-specific gene programs. Notably, distinguishing P . vivax from P . falciparum were a subset of P . vivax sporozoites expressing genes associated with translational regulation and repression. Finally, our comparison of single-cell transcriptomic data from P . vivax sporozoite and erythrocytic forms reveals gene usage patterns unique to sporozoites. In defining the transcriptomic signatures of in idual P . vivax sporozoites, our work provides new insights into the factors driving their developmental trajectory and lays the groundwork for a more comprehensive P . vivax cell atlas.
Genetic classification of Echinococcus granulosus cysts from humans, cattle and camels in Libya using mutation scanning-based analysis of mitochondrial loci
Publisher: Elsevier BV
Date: 12-2010
DOI: 10.1016/J.MCP.2010.07.005
Abstract: We genetically classified Echinococcus granulosus from humans, cattle and camels in Libya utilizing DNA regions (designated pcox1 and pnad1) within the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) mitochondrial genes, respectively. Polymerase chain reaction (PCR)-based single-strand conformation polymorphism (SSCP) analysis of pcox1 and pnad1 licons derived from genomic DNA s les from in idual cysts (n = 176) revealed four distinct electrophoretic profiles for each locus. Direct sequencing of selected licons representing each of these profiles defined four different sequence types for each locus, which were present in five different combinations (designated haplotypes A-E) amongst all 176 isolates. Phylogenetic analysis of concatenated sequence data for these five haplotypes, together with a range of well-defined reference sequences, inferred that all cyst isolates from humans (n = 55) and a small number from cattle (13% of 38) belonged to the G1-G3 complex of E. granulosus (or E. granulosus sensu stricto), whereas most (87%) cysts from cattle and all 83 of them from camels were linked to the G6-G10 complex (or Echinococcus canadensis). The present study provides a foundation for future large-scale studies of the epidemiology and ecology of E. granulosus in Libya and other African countries.
Getting to the guts of the matter: the status and potential of 'omics' research of parasitic protists of the human gastrointestinal system.
Publisher: Elsevier BV
Date: 11-2013
DOI: 10.1016/J.IJPARA.2013.06.005
Abstract: Parasitic protists are a major cause of diarrhoeal illnesses in humans globally. Collectively, enteric pathogens exceed all other forms of infectious disease, in terms of their estimated global prevalence and socioeconomic impact. They have a disproportionately high impact on children in impoverished communities, leading to acute (diarrhoea, vomiting, dehydration and death) and chronic disease (malabsorption, malnutrition, physical and cognitive stunting and predisposition to chronic, non-communicable disease) consequences. However, historically, investment in research and disease control measures has been disproportionately poor, leading to their current classification as neglected pathogens. A sound understanding of their biology is essential in underpinning detection, treatment and control efforts. One major tool in rapidly improving our knowledge of these parasites is the use of biological systems, including 'omic' technologies. In recent years, these tools have shown significant success when applied to enteric protists. This review summarises much of this knowledge and highlights the significant remaining knowledge gaps. A major focus of the present review was to provide a perspective on a way forward to address these gaps using advanced biotechnologies.
Transcriptomic Resources for Parasitic Nematodes of Veterinary Importance
Publisher: Elsevier BV
Date: 2019
Abstract: Parasitic nematodes are important pathogens of animals, causing diseases that impact on agricultural production worldwide. Research on these worms has been constrained by a lack of genetic and genomic tools. Nonetheless, over the past decade this field has made substantial advances, many of which have been led by transcriptomic sequencing. The present review summarises major transcriptomic studies of veterinary parasitic nematodes in recent years, and comments on overarching themes stemming from this work that inform our understanding of parasitism. Finally, we comment on current, state-of-the-art informatic tools for the analysis of complex worm transcriptomes to extract maximum the molecular information from them.
Cryptosporidium and Giardia taxa in faecal samples from animals in catchments supplying the city of Melbourne with drinking water (2011 to 2015)
Publisher: Springer Science and Business Media LLC
Date: 06-2016
TriTOX: A novel Trichomonas vaginalis assay platform for high-throughput screening of compound libraries
Publisher: Elsevier BV
Date: 04-2021
Is Cryptosporidium from the common wombat (Vombatus ursinus) a new species and distinct from Cryptosporidium ubiquitum?
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.MEEGID.2016.06.028
Abstract: The emerging zoonotic pathogen Cryptosporidium ubiquitum has been found in a variety of mammalian hosts, including humans, throughout the world. Advances in the molecular characterization of this parasite using the sequence of the 60kDa glycoprotein (gp60) gene have allowed the classification of "subtypes". Sequences derived from faecal s les from the common wombat (Vombatus ursinus) have identified a novel gp60 subtype designated here as C. ubiquitum XIIg. Phylogenetic analysis suggests that subtypes of C. ubiquitum can be ided into generalist and specialist groups, which is important when considering the zoonotic potential of C. ubiquitum in the context of drinking water safety.
Molecular-based investigation of Cryptosporidium and Giardia from animals in water catchments in southeastern Australia.
Publisher: Elsevier BV
Date: 04-2013
DOI: 10.1016/J.WATRES.2012.12.027
Abstract: There has been no large-scale systematic molecular epidemiological investigation of the waterborne protozoans, Cryptosporidium or Giardia, in southeastern Australia. Here, we explored, for the first time, the genetic composition of these genera in faecal s les from animals in nine Melbourne Water reservoir areas, collected over a period of two-years. We employed PCR-based single-strand conformation polymorphism (SSCP) and phylogenetic analyses of loci (pSSU and pgp60) in the small subunit (SSU) of ribosomal RNA and 60-kDa glycoprotein (gp60) genes to detect and characterise Cryptosporidium, and another locus (ptpi) in the triose-phosphate isomerase (tpi) gene to identify and characterise Giardia. Cryptosporidium was detected in 2.8% of the 2009 s les examined the analysis of all licons defined 14 distinct sequence types for each of pSSU and pgp60, representing Cryptosporidium hominis (genotype Ib - subgenotype IbA10G2R2), Cryptosporidium parvum (genotype IIa - subgenotypes IIaA15G2R1, IIaA19G2R1, IIaA19G3R1, IIaA19G4R1, IIaA20G3R1, IIaA20G4R1, IIaA20G3R2 and IIaA21G3R1), Cryptosporidium cuniculus (genotype Vb - subgenotypes VbA22R4, VbA23R3, VbA24R3, VbA25R4 and VbA26R4), and Cryptosporidium canis, Cryptosporidium fayeri, Cryptosporidium macropodum and Cryptosporidium ubiquitum as well as six new pSSU sequence types. In addition, Giardia was identified in 3.4% of the s les all 28 distinct ptpi sequence types defined were linked to assemblage A of Giardia duodenalis. Of all 56 sequence types characterised, eight and one have been recorded previously in Cryptosporidium and Giardia, respectively, from humans. In contrast, nothing is known about the zoonotic potential of 35 new genotypes of Cryptosporidium and Giardia recorded here for the first time. Future work aims to focus on estimating the prevalence of Cryptosporidium and Giardia genotypes in humans and a wide range of animals in Victoria and elsewhere in Australia. (Nucleotide sequences reported in this paper are available in the GenBank database under accession nos. KC282952-KC283005).
Long pcr amplification of the entire mitochondrial genome from individual helminths for direct sequencing
Publisher: Springer Science and Business Media LLC
Date: 20-09-2007
Abstract: Exploring mitochondrial (mt) genomes has significant implications for various fundamental research areas, including mt biochemistry and physiology, and, importantly, such genomes provide a rich source of markers for population genetics and systematic studies. Although some progress has been made, there is a paucity of information on mt genomes for many metazoan organisms, particularly invertebrates such as parasitic helminths, which relates mainly to the technical limitations associated with sequencing from tiny amounts of material. In this article, we describe a practical long PCR approach for the lification and subsequent sequencing of the entire mt genome from in idual helminths, which overcomes these limitations. The protocol includes the isolation of genomic DNA, long PCR lification, electrophoresis and sequencing, and takes approximately 1-3 weeks to carry out. The present user-friendly, cost-effective approach has demonstrated utility to the study of a range of parasites, and has the potential to be applied to a wide range of organisms.
Recent advances in the genomic and molecular biology of Giardia
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.ACTATROPICA.2017.09.004
Abstract: Giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. Robust tools for analyzing gene function in this parasite have been developed and a range of genetic tools are now available. These together with public databases have provided insights on the function of different genes in Giardia. In this review we provide a current perspective on different molecular aspects of Giardia related to genomics, regulation of encystation, trophozoite transcriptional responses to physiological and xenobiotic (drug-induced) stress, and mechanisms of drug resistance. We also examine recent insights that have contributed to gain knowledge in the study of VSPs, antigenic variation, epigenetics, DNA repair and in the direct manipulation of gene function in Giardia, with a particular focus on the inducible Cre/loxP system.
Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum
Publisher: Wiley
Date: 16-06-2022
DOI: 10.1111/MEC.16556
Abstract: Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human‐ and ruminant‐derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture (3) there have been multiple genetic exchanges, and most are probably recent (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide ersity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long‐term evolutionary consequences of these events. Our results suggest that increased globalization and close human‐animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host–parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.
A Portrait of the Transcriptome of the Neglected Trematode, Fasciola gigantica-Biological and Biotechnological Implications
Publisher: Public Library of Science (PLoS)
Date: 02-2011
The Mitochondrial Genome of Toxocara canis
Publisher: Public Library of Science (PLoS)
Date: 06-08-2008
The small RNA complement of adult Schistosoma haematobium
Publisher: Public Library of Science (PLoS)
Date: 29-05-2018
Highly sensitive non-isotopic restriction endonuclease fingerprinting of nucleotide variability in the gp60 gene within Cryptosporidium species, genotypes and subgenotypes infective to humans, and its implications
Publisher: Wiley
Date: 05-2010
Abstract: The high-resolution analysis of genetic variation has major implications for the identification of parasites and micro-organisms to species and subspecies as well as for population genetic and epidemiological studies. In this study, we critically assessed the effectiveness of a PCR-based restriction endonuclease fingerprinting (REF) method for the detection of mutations in the 60 kDa glycoprotein gene (gp60) of Cryptosporidium, a genus of parasitic protists of major human and animal health importance globally. This gene displays substantial intraspecific variability in sequence, particularly in a TCA (perfect and imperfect) microsatellite region, is present as a single copy in the nuclear genome and is used widely as a marker in molecular epidemiological studies of Cryptosporidium hominis and C. parvum, the two predominant species that infect humans. The results of this study demonstrated an exquisite capacity of REF to detect nucleotide variability in the gp60 gene within each of the two species. The differentiation of genotypes/subgenotypes based on REF analysis was supported by targeted sequencing, allowing the detection of levels of variation as low as a single-nucleotide transversion for licons of approximately 1 kb in size. The high-throughput potential and relatively low-cost of REF make it a particularly useful tool for large-scale genetic analyses of C. hominis and C. parvum. REF could also be utilized for comparative surveys of genetic variability across large nuclear genomic regions. Such analyses of Cryptosporidium in clinical and environmental s les by REF have important implications for identifying sources of infection, modes of transmission and/or possible infectivity to humans, thus assisting in the surveillance and control of cryptosporidiosis. Given its excellent mutation detection capacity, REF should find broad applicability to various single-copy genes as well as a wide range of other protozoan and metazoan parasites.
Rapid, multiplex-tandem PCR assay for automated detection and differentiation of toxigenic cyanobacterial blooms
Publisher: Elsevier BV
Date: 10-2013
DOI: 10.1016/J.MCP.2013.07.001
Abstract: Cyanobacterial blooms are a major water quality issue and potential public health risk in freshwater, marine and estuarine ecosystems globally, because of their potential to produce cyanotoxins. To date, a significant challenge in the effective management of cyanobacterial has been an inability of classical microscopy-based approaches to consistently and reliably detect and differentiate toxic from non-toxic blooms. The potential of cyanobacteria to produce toxins has been linked to the presence of specific biosynthetic gene clusters. Here, we describe the application of a robotic PCR-based assay for the semi-automated and simultaneous detection of toxin biosynthesis genes of each of the toxin classes characterized to date for cyanobacteria [i.e., microcystins (MCYs), nodularins (NODs), cylindrospermopsins (CYNs) and paralytic shellfish toxins (PSTs)/saxitoxins (SXTs)]. We demonstrated high sensitivity and specificity for each assay using well-characterized, cultured isolates, and establish its utility as a quantitative PCR using DNA, clone and cell-based dilution series. In addition, we used 206 field-collected s les and 100 known negative controls to compare the performance of each assay with conventional PCR and direct toxin detection. We report a diagnostic specificity of 100% and a sensitivity of ≥97.7% for each assay.
Epidemiological evaluation of sewage surveillance as a tool to detect the presence of COVID-19 cases in a low case load setting
Publisher: Elsevier BV
Date: 09-2021
Cryptosporidiosis
Publisher: Oxford University Press
Date: 07-2011
DOI: 10.1093/MED/9780198570028.003.0053
Abstract: Cryptosporidium species represent a genus of parasitic protozoa (Apicomplexa) that are transmitted via the faecal-oral route and commonly infect the epithelial tissues of the gastric or intestinal (or sometimes the respiratory) tract of many vertebrates, including humans. Infection occurs following the ingestion of viable and resistant oocysts, through direct host-to-host contact or in contaminated food, drinking or recreational water. Infection can be transmitted via anthroponotic (human-to-human, human-to-animal) or zoonotic (animal-to-human or animal-to-animal) pathways, depending upon the species of Cryptosporidium. Although infection can be asymptomatic, common symptoms of disease (cryptosporidiosis) include diarrhoea, colic (abdominal pain), nausea or vomiting, dehydration and/or fever. In humans, cryptosporidial infection in immunocompetent patients is usually short-lived (days to weeks) and eliminated following the stimulation of an effective immune response. However, infection in immunodeficient in iduals (e.g., those with HIV/AIDS) can be chronic and fatal (in the absence of immunotherapy), as there are few effective anti-cryptosporidial drugs and no vaccines available. The present chapter provides an account of the history, taxonomy and biology, genomics and genetics of Cryptosporidium, the epidemiology, pathogenesis, treatment and control of cryptosporidiosis and the advances in tools for the identification and characterisation of Cryptosporidium species and the diagnosis of cryptosporidiosis.
VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses
Publisher: Oxford University Press (OUP)
Date: 09-2022
Abstract: Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an in idual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of ersity and selection, and 3D visualization of genotypic information encoded in Variant Call Format on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritizing targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum, revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.
Analysis of the genetic diversity within Cryptosporidium hominis and Cryptosporidium parvum from imported and autochtonous cases of human cryptosporidiosis by mutation scanning
Publisher: Wiley
Date: 11-2008
Abstract: The present study investigated sequence variation in part of the 60 kilodalton glycoprotein (pgp60) gene among Cryptosporidium hominis and Cryptosporidium parvum isolates (n=115) from citizens of the UK inferred to have been infected whilst travelling abroad (to 25 countries) or in the UK. The genomic DNA s les from these isolates were subjected to PCR-coupled single-strand conformation polymorphism analysis, followed by targeted sequencing of pgp60. In idual s les were classified to the genotypic and subgenotypic levels based on phylogenetic analysis (Bayesian inference) of pgp60 data, including published sequences for comparison. Based on this analysis, five C. hominis (Ia-If) and four C. parvum (IIa, IIc-IIe) genotypes were identified, equating to 16 and 10 subgenotypes, respectively. Of these genotypes, C. hominis Ib was predominant (n=82). Interestingly, one subgenotype (C. hominis Ib A10G2R2) accounted for the majority of the s les examined and was identified in travellers to 14 countries the examination of published records suggested that C. hominis Ib A10G2R2 has a global distribution. Numerous new and seemingly rare subgenotypes (eight for C. hominis and six for C. parvum) were also discovered. In conclusion, the present study revealed substantial genetic variation in pgp60 within both C. hominis and C. parvum and emphasizes the need to undertake investigations of human and animal populations in countries for which there is no information on the genetic make-up of Cryptosporidium infecting humans.
Molecular characterization of Thelastomatoidea (Nematoda: Oxyurida) from cockroaches in Australia
Publisher: Cambridge University Press (CUP)
Date: 27-03-2006
Corrigendum to “Toward next-generation sequencing of mitochondrial genomes — Focus on parasitic worms of animals and biotechnological implications” [Biotechnol. Adv. 28 (2010) 151–159]
Publisher: Elsevier BV
Date: 03-2010
The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum – two hookworms of animal health and zoonotic importance
Publisher: Springer Science and Business Media LLC
Date: 11-02-2009
Abstract: Hookworms are blood-feeding nematodes that parasitize the small intestines of many mammals, including humans and cattle. These nematodes are of major socioeconomic importance and cause disease, mainly as a consequence of anaemia (particularly in children or young animals), resulting in impaired development and sometimes deaths. Studying genetic variability within and among hookworm populations is central to addressing epidemiological and ecological questions, thus assisting in the control of hookworm disease. Mitochondrial (mt) genes are known to provide useful population markers for hookworms, but mt genome sequence data are scant. The present study characterizes the complete mt genomes of two species of hookworm, Ancylostoma caninum (from dogs) and Bunostomum phlebotomum (from cattle), each sequenced (by 454 technology or primer-walking), following long-PCR lification from genomic DNA (~20–40 ng) isolated from in idual adult worms. These mt genomes were 13717 bp and 13790 bp in size, respectively, and each contained 12 protein coding, 22 transfer RNA and 2 ribosomal RNA genes, typical for other secernentean nematodes. In addition, phylogenetic analysis (by Bayesian inference and maximum likelihood) of concatenated mt protein sequence data sets for 12 nematodes (including Ancylostoma caninum and Bunostomum phlebotomum ), representing the Ascaridida, Spirurida and Strongylida, was conducted. The analysis yielded maximum statistical support for the formation of monophyletic clades for each recognized nematode order assessed, except for the Rhabditida. The mt genomes characterized herein represent a rich source of population genetic markers for epidemiological and ecological studies. The strong statistical support for the construction of phylogenetic clades and consistency between the two different tree-building methods employed indicate the value of using whole mt genome data sets for systematic studies of nematodes. The grouping of the Spirurida and Ascaridida to the exclusion of the Strongylida was not supported in the present analysis, a finding which conflicts with the current evolutionary hypothesis for the Nematoda based on nuclear ribosomal gene data.
Analysis of genetic variation in Globocephaloides populations from macropodid marsupials using a mutation scanning-based approach
Publisher: Wiley
Date: 08-2009
Abstract: Three species of Globocephaloides, parasitic nematodes occurring in macropodid marsupials in different areas of Australia, were characterized by the sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA. S les were subjected to PCR-coupled SSCP analysis and targeted sequencing, in order to assess genetic variation within and among in iduals from different host species. Both SSCP and sequence data supported the current classification of morphospecies. Contrary to a previous hypothesis that cryptic species exist within the Globocephaloides trifidospicularis "complex", no or minor (0.2%) variation was detected among in iduals from different hosts or geographical origins. Within G. macropodis populations, there was a consistent difference in both the ITS-1 (5.2%) and ITS-2 (7.1%) sequences between in iduals derived from Macropus agilis and those from Macropus dorsalis. Although the results suggested that G. macropodis from each host species represented sibling species, future morphological study of in iduals representing each G. macropodis genotype is warranted to provide further support for this hypothesis. (Nucleotide sequence data have been deposited in the GenBank database under accession nos. GQ131400-GQ131409.).
First molecular characterization of Cryptosporidium and Giardia from bovines (Bos taurus and Bubalus bubalis) in Sri Lanka: unexpected absence of C. parvum from pre-weaned calves
Publisher: Springer Science and Business Media LLC
Date: 21-02-2014
Elucidating the transcriptome of Fasciola hepatica - A key to fundamental and biotechnological discoveries for a neglected parasite
Publisher: Elsevier BV
Date: 03-2010
DOI: 10.1016/J.BIOTECHADV.2009.12.003
Abstract: Liver flukes of animals are parasitic flatworms (Platyhelminthes: Digenea) of major socioeconomic importance in many countries. Key representatives, such as Fasciola hepatica and F. gigantica, cause "liver fluke disease" (= fascioliasis), which is of major animal health significance worldwide. In particular, F. hepatica is a leading cause of production losses to the livestock (mainly sheep and cattle) and meat industries due to clinical disease, reduced weight gain and milk production, and deaths. This parasite is also a major food-borne pathogen of humans throughout parts of the Middle East, Asia and South America. Currently, there is a significant focus on the development of new approaches for the prevention and control of fascioliasis in livestock. Recent technological advances in genomics and bioinformatics provide unique opportunities for the identification and prevalidation of drug targets and vaccines through a better understanding of the biology of F. hepatica and related species as well as their relationship with their hosts at the molecular level. Surprisingly, despite the widespread socioeconomic impact of fascioliasis, genomic datasets for F. hepatica are scant, limiting the molecular biological research of this parasite. The present article explores specifically the transcriptome of the adult stage of F. hepatica using an integrated genomic-bioinformatic platform. The analysis of the current data reveals numerous molecules of biological relevance, some of which are inferred to be involved in key biological processes or pathways that could serve as targets for new trematocidal drugs or vaccines. Improved insights into the transcriptome of F. hepatica should pave the way for future, comparative analysis of the transcriptomes of other developmental stages of this and related parasites, such as F. gigantica, cancer-causing flatworms (Clonorchis sinensis and Opisthorchis viverrini) and blood flukes (Schistosoma mansoni and S. japonicum). Prediction of the essentiality of genes and their products, molecular network connectivity of trematode genes as well as experimental exploration of function should also add value to the genomic discovery efforts in the future, focused on biotechnological outcomes.
Unlocking the Transcriptomes of Two Carcinogenic Parasites, Clonorchis sinensis and Opisthorchis viverrini
Publisher: Public Library of Science (PLoS)
Date: 22-06-2010
Comparative genomics of Cylindrospermopsis raciborskii strains with differential toxicities
Publisher: Springer Science and Business Media LLC
Date: 29-01-2014
A self-sufficient pressure pump using latex balloons for microfluidic applications
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8LC00471D
Abstract: Here, we demonstrate a self-sufficient, inexpensive and disposable pressure pump using commercially available latex balloons.
Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes
Publisher: Elsevier BV
Date: 10-2014
DOI: 10.1016/J.IJPARA.2014.06.005
Abstract: Despite right open reading frame kinases (RIOKs) being essential for life, their functions, substrates and cellular pathways remain enigmatic. In the present study, gene structures were characterised for 26 RIOKs from draft genomes of parasitic and free-living nematodes. RNA-seq transcription profiles of riok genes were investigated for selected parasitic nematodes and showed that these kinases are transcribed in developmental stages that infect their mammalian host. Three-dimensional structural models of Caenorhabditis elegans RIOKs were predicted, and elucidated functional domains and conserved regions in nematode homologs. These findings provide prospects for functional studies of riok genes in C. elegans, and an opportunity for the design and validation of nematode-specific inhibitors of these enzymes in socioeconomic parasitic worms.
Genetic categorization of Echinococcus granulosus from humans and herbivorous hosts in Iran using an integrated mutation scanning-phylogenetic approach
Publisher: Wiley
Date: 08-2009
Abstract: In the present study, we have extended earlier taxonomic, biochemical and experimental investigations to characterize Echinococcus granulosus from various hosts in Iran utilizing DNA regions (designated pcox1 and pnad1) within the cytochrome c oxidase subunit 1 and NADH dehydrogenase 1 mitochondrial genes, respectively. An emphasis was placed on the characterization of E. granulosus isolates (cyst material) from humans, sheep, goats, cattle and camels, and on assessing their genetic relationships. PCR-based SSCP analysis of pcox1 and pnad1 licons derived from in idual isolates (n=148) of E. granulosus revealed five (pc1-pc5) and nine (pn1-pn9) electrophoretic profiles, respectively. Sequencing of pcox1 and pnad1 licons representing unique SSCP profiles demonstrated that each profile was linked unequivocally to a particular sequence and that single point mutations were readily detectable by SSCP. Phylogenetic analyses of pcox1 and/or pnad1 nucleotide sequence data were conducted using Bayesian inference and maximum likelihood tree-building methods. Following the phylogenetic analyses of concatenated pcox1+pnad1 sequence data, including representatives of all presently recognized Echinococcus species/genotypes as well as Taenia saginata (as the outgroup), the majority of cyst isolates (142 of 148 95.9%) from humans, ruminants (sheep, goats and cattle) and camels were assigned to the G1-G3 complex of E. granulosus (or E. granulosus sensu stricto), whereas some E. granulosus cysts (6 of 19 31.6%) from camels were assigned to the G6-G10 complex (or E. canadensis). The present study reinforces the advantages of the mutation scanning-sequencing-phylogenetic approach to explore variation in multiple mitochondrial loci within and among Echinococcus populations, which provides a platform for future, detailed studies of the molecular epidemiology of E. granulosus in Iran and other countries. (Note: The sequences determined in the present study have been deposited in the GenBank database under accession numbers: FJ796203-FJ796207 (pcox1) and FJ796208-FJ796216 (pnad1)).
Flatworms have lost the right open reading frame kinase 3 gene during evolution
Publisher: Springer Science and Business Media LLC
Date: 15-05-2015
DOI: 10.1038/SREP09417
Abstract: All multicellular organisms studied to date have three ri ght o pen reading frame kinase genes (designated riok-1 , riok-2 and riok-3 ). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins.
Wastewater monitoring for SARS-CoV-2
Publisher: CSIRO Publishing
Date: 2021
DOI: 10.1071/MA21006
Abstract: Wastewater monitoring (WM) of SARS-CoV-2 from sewers was applied throughout the world early in the COVID-19 pandemic. Sharing of protocols and experiences in WM of SARS-CoV-2 by national and international researchers and practitioners has been vital to ensuring the sensitivity and specificity of the methods. WM has been a valuable adjunct to human clinical testing, and when positive results occur in sewage, community testing has been increased. WM findings allow public health officials to track and respond to the impacts of loosening lockdown restrictions, demonstrating when return to normal social activities might occur without a resurgence of rapid community transmission, and they are particularly useful in areas with low human case numbers and/or low clinical testing rates. New research is required to address several practical knowledge gaps, for ex le, s ling protocols, prediction of case prevalence from viral numbers by modelling, and determination of detection limits. Communication to the Australian public of WM of SARS-CoV-2 has been via interactive, visual dashboards. Once SARS-CoV-2 vaccinations are introduced, WM could help track the underlying circulation of the virus in the population, the spread of known variants and its future evolution.
Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections
Publisher: Public Library of Science (PLoS)
Date: 26-07-2021
DOI: 10.1371/JOURNAL.PNTD.0009597
Abstract: Soil-transmitted helminths, such as roundworms ( Ascaris lumbricoides ), whipworms ( Trichuris trichiura ) and hookworms ( Necator americanus and Ancylostoma spp.), are gastrointestinal parasites that occur predominantly in low- to middle-income countries worldwide and disproportionally impact children. Depending on the STH species, health status of the host and infection intensity, direct impacts of these parasites include malnutrition, anaemia, diarrhoea and physical and cognitive stunting. The indirect consequences of these infections are less well understood. Specifically, gastrointestinal infections may exert acute or chronic impacts on the natural gut microfauna, leading to increased risk of post-infectious gastrointestinal disorders, and reduced gut and overall health through immunomodulating mechanisms. To date a small number of preliminary studies have assessed the impact of helminths on the gut microbiome, but these studies are conflicting. Here, we assessed STH burden in 273 pre-school and school-aged children in Tha Song Yang district, Tak province, Thailand receiving annual oral mebendazole treatment. Ascaris lumbricoides (107/273) and Trichuris trichiura (100/273) were the most prevalent species and often occurred as co-infections (66/273). Ancylostoma ceylanicum was detected in a small number of children as well ( n = 3). All of these infections were of low intensity ( ,999 or 999 eggs per gram for Ascaris and Trichuris respectively). Using this information, we characterised the baseline gut microbiome profile and investigated acute STH-induced alterations, comparing infected with uninfected children at the time of s ling. We found no difference between these groups in bacterial alpha- ersity, but did observe differences in beta- ersity and specific differentially abundant OTUs, including increased Akkermansia muciniphila and Bacteroides coprophilus , and reduced Bifidobacterium adolescentis , each of which have been previously implicated in STH-associated changes in the gut microfauna.
Eukaryote-conserved methylarginine is absent in diplomonads and functionally compensated in Giardia
Publisher: Oxford University Press (OUP)
Date: 23-07-2020
Abstract: Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis—a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly erged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and ersification of these key networks in higher eukaryotes.
Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites
Publisher: Public Library of Science (PLoS)
Date: 31-07-2017
Self-sufficient, low-cost microfluidic pumps utilising reinforced balloons
Publisher: Royal Society of Chemistry (RSC)
Date: 2019
DOI: 10.1039/C9LC00618D
Abstract: Reinforcing a latex balloon with nylon stockings leads to a high pressure self-sufficient pump, which is used for studying the mechanobiology of aortic cells and hydrodynamic capturing of large human monocytes.
Transcriptomic analysis of albendazole resistance in human diarrheal parasite Giardia duodenalis
Publisher: Elsevier BV
Date: 08-2023
Decoding the Ascaris suum Genome using Massively Parallel Sequencing and Advanced Bioinformatic Methods – Unprecedented Prospects for Fundamental and Applied Research
Publisher: Elsevier
Date: 2013
Exploration of extracellular vesicles from Ascaris suum provides evidence of parasite–host cross talk
Publisher: Wiley
Date: 14-02-2019
Sequence diversity and evolution of an iflavirus family associated with ticks
Publisher: Cold Spring Harbor Laboratory
Date: 03-06-2020
DOI: 10.1101/2020.06.02.129551
Abstract: We studied a family of iflaviruses, a group of RNA viruses frequently found in arthropods, focusing on viruses associated with ticks. Our aim was to bring insight on the evolutionary dynamics of this group of viruses, which may interact with the biology of ticks. We explored systematically de novo RNA-Seq assemblies available for species of ticks which allowed to identify nine new genomes of iflaviruses. The phylogeny of virus sequences was not congruent with that of the tick hosts, suggesting recurrent host changes across tick genera along evolution. We identified five different variants with a complete or near-complete genome in Ixodes ricinus. These sequences were closely related, which allowed a fine-scale estimation of patterns of substitutions: we detected a strong excess of synonymous mutations suggesting evolution under strong positive selection. ISIV, a sequence found in the ISE6 cell line of Ixodes scapularis, was unexpectedly nearidentical with I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.
Monoaminergic signaling as a target for anthelmintic drug discovery: Receptor conservation among the free-living and parasitic nematodes
Publisher: Elsevier BV
Date: 05-2012
Corrigendum: Responses of the differentiated intestinal epithelial cell line Caco-2 to infection with the Giardia intestinalis GS isolate [Front. Cell. Infect. Microbiol., 8, (2018), (244)] DOI: 10.3389/fcimb.2018.00244
Publisher: Frontiers Media SA
Date: 24-08-2018
Specific and genotypic identification ofCryptosporidium from a broad range of host species by nonisotopic SSCP analysis of nuclear ribosomal DNA
Publisher: Wiley
Date: 08-2007
Abstract: The accurate identification of Cryptosporidium (Protozoa: Apicomplexa) species and genotypes is central to the understanding of the transmission and to the diagnosis and control of cryptosporidiosis. In this study, we demonstrate the effectiveness of nonisotopic SSCP analysis of a approximately 300 bp region of the small subunit (pSSU) of ribosomal DNA for the specific identification of and delineation among 18 different Cryptosporidium species and genotypes from a wide range of hosts. This mutation scanning approach allowed the rapid and reliable differentiation between species/genotypes differing by as little as 1.3% in the pSSU sequence, with the capacity to detect point mutations. The present findings confirm the usefulness of this tool for the rapid genetic screening of Cryptosporidium s les from any host species, providing a foundation for detailed systematic, epidemiological and ecological studies. Although applied herein to pSSU, this low cost approach should be applicable to a wide range of genetic loci for population genetic investigations of Cryptosporidium.
Giardia/giardiasis - A perspective on diagnostic and analytical tools
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.BIOTECHADV.2013.10.009
Abstract: Giardiasis is a gastrointestinal disease of humans and other animals caused by species of parasitic protists of the genus Giardia. This disease is transmitted mainly via the faecal-oral route (e.g., in water or food) and is of socioeconomic importance worldwide. The accurate detection and genetic characterisation of the different species and population variants (usually referred to as assemblages and/or sub-assemblages) of Giardia are central to understanding their transmission patterns and host spectra. The present article provides a background on Giardia and giardiasis, and reviews some key techniques employed for the identification and genetic characterisation of Giardia in biological s les, the diagnosis of infection and the analysis of genetic variation within and among species of Giardia. Advances in molecular techniques provide a solid basis for investigating the systematics, population genetics, ecology and epidemiology of Giardia species and genotypes as well as the prevention and control of giardiasis.
High resolution melting-curve (HRM) analysis for the diagnosis of cryptosporidiosis in humans
Publisher: Elsevier BV
Date: 02-2009
DOI: 10.1016/J.MCP.2008.10.003
Abstract: Cryptosporidiosis of humans is an intestinal disease caused predominantly by infection with Cryptosporidium hominis or C. parvum. This disease is transmitted mainly via the faecal-oral route (water or food) and has major socioeconomic impact globally. The diagnosis and genetic characterization of the main species and population variants (also called "genotypes" and "subgenotypes") of Cryptosporidium infecting humans is central to the prevention, surveillance and control of cryptosporidiosis, particularly as there is presently no cost effective anti-cryptosporidial chemotherapeutic regimen or vaccine available. In the present study, we established a polymerase chain reaction (PCR)-coupled high resolution melting-curve (HRM) analysis method, utilizing the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA as the genetic marker, for the diagnosis of Cryptosporidium hominis, C. parvum or C. meleagridis infection. An evaluation of the method revealed intra- and inter-assay variabilities of <1.5 and 3.5%, respectively. Cryptosporidium hominis, C. parvum and C. meleagridis were detected in 97, 44 and 2, respectively, of the 143 Cryptosporidium oocyst DNA s les originating from Australians with clinical cryptosporidiosis. The melting profiles characterized by peaks of 72.47+/-0.33 degrees C and 74.19+/-0.45 degrees C (profile 1), 72.17+/-0.32 degrees C (profile 2) and 73.33+/-0.03 degrees C (profile 3) genetically identified as C. hominis, C. parvum and C. meleagridis, respectively. In conclusion, PCR-coupled melting analysis of ITS-2 achieved the diagnosis of Cryptosporidium hominis, C. parvum or C. meleagridis infection. This approach is well suited for the rapid screening of large numbers of Cryptosporidium oocyst DNA s les and, although qualitative, is significantly less time-consuming to carry out than electrophoretic analysis and has the added advantage of data storage and analysis capabilities in silico. This method provides a useful tool for investigating the epidemiology and outbreaks of cryptosporidiosis, and could be applicable to species of Cryptosporidium other than those investigated herein.
Molecular Changes in Opisthorchis viverrini (Southeast Asian Liver Fluke) during the Transition from the Juvenile to the Adult Stage
Publisher: Public Library of Science (PLoS)
Date: 29-11-2012
The Thelastomatoidea (Nematoda: Oxyurida) of two sympatric Panesthiinae (Insecta: Blattodea) from southeastern Queensland, Australia: taxonomy, species richness and host specificity
Publisher: Brill
Date: 2005
DOI: 10.1163/156854105774384741
Abstract: The thelastomatoid fauna of two species of wood-burrowing cockroach (Blattodea, Blaberidae), Panesthia cribrata and Panesthia tryoni tryoni, from Lamington National Park, Australia, is described. The following eight new species and three new genera of thelastomatid are proposed: Bilobostoma exerovulva n. g., n. sp. Cordonicola gibsoni n. sp. Coronostoma australiae n. sp. Desmicola ornata n. sp. Hammerschmidtiella hochi n. sp. Malaspinanema goateri n. g., n. sp. Travassosinema jaidenae n. sp. and Tsuganema cribratum n. g., n. sp. Additional data are given for Blattophila sphaerolaima and Leidynemella fusiformis. Of the 11 species reported, nine were found in P. cribrata and ten in P. tryoni tryoni. Such levels of thelastomatoid species richnessness in single host species are exceptional. Only the mole cricket, Gryllotalpa africana (23), and the domestic cockroach, Periplaneta americana (20), have higher reported richness. Three species, T. jaidenae, C. australiae and D. ornata, were found either exclusively or significantly more prevalently in P. tryoni tryoni than in P. cribrata. Species of Travassosinema, Coronostoma and Desmicola have been found previously only in millipedes (Diplopoda), a fact that suggests that there is a greater degree of niche overlap between P. tryoni tryoni and millipedes than for P. cribrata.
Genetic analysis of Giardia and Cryptosporidium from people in Northern Australia using PCR-based tools
Publisher: Elsevier BV
Date: 12-2015
DOI: 10.1016/J.MEEGID.2015.08.034
Abstract: To date, there has been limited genetic study of the gastrointestinal pathogens Giardia and Cryptosporidium in northern parts of Australia. Here, PCR-based methods were used for the genetic characterization of Giardia and Cryptosporidium from 695 people with histories of gastrointestinal disorders from the tropical North of Australia. Genomic DNAs from fecal s les were subjected to PCR-based analyses of regions from the triose phosphate isomerase (tpi), small subunit (SSU) of the nuclear ribosomal RNA and/or the glycoprotein (gp60) genes. Giardia and Cryptosporidium were detected in 13 and four of the 695 s les, respectively. Giardia duodenalis assemblages A and B were found in 4 (31%) and 9 (69%) of the 13 s les in persons of <9 years of age. Cryptosporidium hominis (subgenotype IdA18), Cryptosporidium mink genotype (subgenotype IIA16R1) and C. felis were also identified in single patients of 11-21 years of age. Future studies might focus on a comparative study of these and other protists in rural communities in Northern Australia.
Detection of diarrhoeal pathogens in human faeces using an automated, robotic platform
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.MCP.2011.10.004
Abstract: Infectious diarrhoeal diseases represent a major socio-economic burden to humans, and are linked to a range of pathogens, including viruses, bacteria and protists. The accurate detection of such pathogens is central to control. However, detection often relies on methods that have limited diagnostic sensitivity and specificity. Here, we assessed an automated, robotic platform for the simultaneous detection of eight major pathogens associated with infectious diarrhoea. Genomic DNA s les (n = 167) from faeces from humans with diarrhoea and diagnosed as cryptosporidiosis, and 100 uninfected control subjects, were tested for adenovirus 40/41, norovirus, Clostridium difficile, C ylobacter, Salmonella, Shigella, Cryptosporidium and Giardia by multiplexed-tandem PCR, and also characterized by single-strand conformation polymorphism analysis (SSCP) and selective sequencing. All 167 s les tested positive for Cryptosporidium, five for adenovirus 40/41, four for C ylobacter, three for C. difficile and seven for Shigella spp., with no false positive results for any assay. The automated PCR exhibited a high sensitivity, with <10 in idual pathogens being readily detected. The robotic detection platform assessed here represents a sensitive, high-throughput tool for key pathogens linked to infectious diarrhoea in humans. This platform requires little molecular biological expertise and is well suited to various diagnostic facilities and settings.
Low cost whole-organism screening of compounds for anthelmintic activity
Publisher: Elsevier BV
Date: 04-2015
DOI: 10.1016/J.IJPARA.2015.01.007
Abstract: Due to major problems with drug resistance in parasitic nematodes of animals, there is a substantial need and excellent opportunities to develop new anthelmintics via genomic-guided and/or repurposing approaches. In the present study, we established a practical and cost-effective whole-organism assay for the in vitro-screening of compounds for activity against parasitic stages of the nematode Haemonchus contortus (barber's pole worm). The assay is based on the use of exsheathed L3 (xL3) and L4 stages of H. contortus of small ruminants (sheep and goats). Using this assay, we screened a panel of 522 well-curated kinase inhibitors (GlaxoSmithKline, USA code: PKIS2) for activity against H. contortus by measuring the inhibition of larval motility using an automated image analysis system. We identified two chemicals within the compound classes biphenyl amides and pyrazolo[1,5-α]pyridines, which reproducibly inhibit both xL3 and L4 motility and development, with IC50s of 14-47 μM. Given that these inhibitors were designed as anti-inflammatory drugs for use in humans and fit the Lipinski rule-of-five (including bioavailability), they show promise for hit-to-lead optimisation and repurposing for use against parasitic nematodes. The screening assay established here has significant advantages over conventional methods, particularly in terms of ease of use, throughput, time and cost. Although not yet fully automated, the current assay is readily suited to the screening of hundreds to thousands of compounds for subsequent hit-to-lead optimisation. The current assay is highly adaptable to many parasites of socioeconomic importance, including those causing neglected tropical diseases. This aspect is of major relevance, given the urgent need to deliver the goals of the London Declaration (esource/london-declaration) through the rapid and efficient repurposing of compounds in public-private partnerships.
Development and validation of a multiplexed-tandem qPCR tool for diagnostics of human soil-transmitted helminth infections
Publisher: Public Library of Science (PLoS)
Date: 17-06-2019
Aoruroides queenslandensis n. sp. (Oxyurida: Thelastomatoidea), a new nematode from Australian Panesthiinae (Blattodea: Blaberidae)
Publisher: Springer Science and Business Media LLC
Date: 09-2004
VIVID: a web application for variant interpretation and visualisation in multidimensional analyses
Publisher: Cold Spring Harbor Laboratory
Date: 19-11-2021
DOI: 10.1101/2021.11.16.468904
Abstract: Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an in idual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of ersity and selection, and 3-dimensional (3D) visualisation of genotypic information encoded in Variant Call Format (VCF) on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritising targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum , revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.
Asynchronous generation of oil droplets using a microfluidic flow focusing system
Publisher: Springer Science and Business Media LLC
Date: 22-07-2019
DOI: 10.1038/S41598-019-47078-8
Abstract: Here, we show that long-term exposure of PDMS based microfluidic droplet generation systems to water can reverse their characteristics such that they generate oil-in-water droplets instead of water-in-oil droplets. The competition between two oil columns entering via the two side channels leads to asynchronous generation of oil droplets. We identify various modes of droplet generation, and study the size, gap and generation rate of droplets under different combinations of oil and water pressures. Oil droplets can also be generated using syringe pumps, various oil viscosities, and different combinations of immiscible liquids. We also demonstrate the ability to dynamically change the gap between the oil droplets from a few hundred microns to just a few microns in successive cycles using a latex balloon pressure pump. This method requires no special equipment or chemical treatments, and importantly can be reversed by long-term exposure of the PDMS surfaces to the ambient air.
Bioinformatics meets parasitology
Publisher: Wiley
Date: 09-04-2012
DOI: 10.1111/J.1365-3024.2011.01304.X
Abstract: The advent and integration of high-throughput '-omics' technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For ex le, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next-generation sequencing technologies and bioinformatic tools to large-scale investigations of the transcriptomes of parasitic nematodes of socio-economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention.
Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut
Publisher: American Society for Microbiology
Date: 13-04-2023
DOI: 10.1128/SPECTRUM.03671-22
Abstract: The malaria parasite Plasmodium falciparum causes more than half a million deaths per year. The current treatment regimen targets the symptom-causing blood stage inside the human host.
Tunable Harmonic Flow Patterns in Microfluidic Systems through Simple Tube Oscillation
Publisher: Wiley
Date: 10-2020
Assessing calves as carriers of Cryptosporidium and Giardia with zoonotic potential on dairy and beef farms within a water catchment area by mutation scanning.
Publisher: Wiley
Date: 08-2013
Abstract: In the present study, we undertook a molecular epidemiological survey of Cryptosporidium and Giardia in calves on three dairy and two beef farms within an open drinking water catchment area (Melbourne, Australia). Faecal s les (n = 474) were collected from calves at two time points (5 months apart) and tested using a PCR-based mutation scanning-targeted sequencing phylogenetic approach, employing regions within the genes of small subunit (SSU) of ribosomal RNA (designated partial SSU), 60 kDa glycoprotein (pgp60) and triose phosphate isomerase (ptpi) as genetic markers. Using partial SSU, the C. bovis, C. parvum, C. ryanae and a new genotype of Cryptosporidium were characterised from totals of 74 (15.6%), 35 (7.3%), 37 (7.8%) and 9 (1.9%) s les, respectively. Using pgp60, C. parvum genotype IIa subgenotype A18G3R1 was detected in 29 s les. Using ptpi, G. duodenalis assemblages A and E were detected in totals of 10 (2.1%) and 130 (27.4%) s les, respectively. The present study showed that a considerable proportion of dairy and beef calves in this open water catchment region excreted Cryptosporidium (i.e. subgenotype IIaA18G3R1) and Giardia (e.g. assemblage A) that are consistent with those infecting humans, inferring that they are of zoonotic importance. Future work should focus on exploring, in a temporal and spatial way, whether these parasites occur in the environment and water of the catchment reservoir.
A first insight into the genotypes of Echinococcus granulosus from humans in Mongolia
Publisher: Elsevier BV
Date: 02-2011
DOI: 10.1016/J.MCP.2010.11.001
Abstract: Polymerase chain reaction (PCR)-based single-strand conformation polymorphism (SSCP) and targeted sequencing were employed to genetically classify Echinococcus granulosus cysts from humans from 12 provinces in Mongolia using two DNA loci, designated pcox-1 and pnad-1, within the mitochondrial cytochrome c oxidase subunit 1 (cox-1) and NADH dehydrogenase subunit 1 (nad-1) genes, respectively. SSCP analysis of pcox-1 and pnad-1 licons produced from genomic DNA s les from in idual E. granulosus cysts (n = 50) from in idual humans displayed four distinct electrophoretic profiles for each pcox-1 and pnad-1. The direct sequencing of selected licons representing each of these profiles defined four distinct sequence types for each locus, present in four different combinations (designated as haplotypes M1-M4) for all 50 cyst isolates. Phylogenetic analysis of concatenated sequence data for these four haplotypes, including well-defined reference sequences, inferred that 68% of the cyst isolates belonged to the G1-G3 complex of E. granulosus (or E. granulosus sensu stricto), whereas the remaining (32%) were linked to the G6-G10 complex (or Echinococcus canadensis). Humans infected with E. granulosus cysts of the G1-G3 complex originated mainly from the eastern regions of Mongolia, whereas those harbouring cysts of the G6-G10 complex were from the western part of this country. The present study provides a first glimpse of the genetic composition of E. granulosus from humans in Mongolia, and forms a foundation for future studies of the epidemiology and ecology of the parasite(s) in animals and humans in this and surrounding countries.
Long-read assembly and comparative evidence-based reanalysis ofCryptosporidiumgenome sequences reveal new biological insights
Publisher: Cold Spring Harbor Laboratory
Date: 29-01-2020
DOI: 10.1101/2021.01.29.428682
Abstract: Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community still relies on a fragmented reference genome sequence from 2004. Incomplete reference sequences h er experimental design and interpretation. We have generated a new C. parvum IOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species C. parvum , C. hominis and C. tyzzeri . The new C. parvum IOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers 13 of 16 possible telomeres and raises a new hypothesis for the remaining telomeres and associated subtelomeric regions. Comparative annotation revealed that most “missing” orthologs are found suggesting that species differences result primarily from structural rearrangements, gene copy number variation and SNVs in C. parvum, C. hominis and C. tyzzeri . We made ,500 C. parvu m annotation updates based on experimental evidence. They included new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete DNA methylase Dnmt2 ortholog. 190 genes under positive selection including many new candidates were identified using the new assembly and annotation as reference. Finally, possible subtelomeric lification and variation events in C. parvum are detected that reveal a new level of genome plasticity that will both inform and impact future research.
Comparative genomics revealed adaptive admixture in cryptosporidium hominis in Africa
Publisher: Microbiology Society
Date: 2021
Abstract: Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and is associated with childhood mortality, malnutrition, cognitive development and growth retardation. Cryptosporidium hominis is the dominant pathogen in Africa, and genotyping at the glycoprotein 60 ( gp60 ) gene has revealed a complex distribution of different subtypes across this continent. However, a comprehensive exploration of the metapopulation structure and evolution based on whole-genome data has yet to be performed. Here, we sequenced and analysed the genomes of 26 C . hominis isolates, representing different gp60 subtypes, collected at rural sites in Gabon, Ghana, Madagascar and Tanzania. Phylogenetic and cluster analyses based on single-nucleotide polymorphisms showed that isolates predominantly clustered by their country of origin, irrespective of their gp60 subtype. We found a significant isolation-by-distance signature that shows the importance of local transmission, but we also detected evidence of hybridization between isolates of different geographical regions. We identified 37 outlier genes with exceptionally high nucleotide ersity, and this group is significantly enriched for genes encoding extracellular proteins and signal peptides. Furthermore, these genes are found more often than expected in recombinant regions, and they show a distinct signature of positive or balancing selection. We conclude that: (1) the metapopulation structure of C. hominis can only be accurately captured by whole-genome analyses (2) local anthroponotic transmission underpins the spread of this pathogen in Africa (3) hybridization occurs between distinct geographical lineages and (4) genetic introgression provides novel substrate for positive or balancing selection in genes involved in host–parasite coevolution.
Corrigendum to “Profiling circulating miRNAs in serum from pigs infected with the porcine whipworm, Trichuris suis” [Vet. Parasitol. 223 (2016) 30–33], (S0304401716300772), (10.1016/j.vetpar.2016.03.025))
Publisher: Elsevier BV
Date: 2018
Phylogenomic and biogeographic reconstruction of the Trichinella complex
Publisher: Springer Science and Business Media LLC
Date: 02-2016
DOI: 10.1038/NCOMMS10513
Abstract: Trichinellosis is a globally important food-borne parasitic disease of humans caused by roundworms of the Trichinella complex. Extensive biological ersity is reflected in substantial ecological and genetic variability within and among Trichinella taxa, and major controversy surrounds the systematics of this complex. Here we report the sequencing and assembly of 16 draft genomes representing all 12 recognized Trichinella species and genotypes, define protein-coding gene sets and assess genetic differences among these taxa. Using thousands of shared single-copy orthologous gene sequences, we fully reconstruct, for the first time, a phylogeny and biogeography for the Trichinella complex, and show that encapsulated and non-encapsulated Trichinella taxa erged from their most recent common ancestor ∼21 million years ago (mya), with taxon ersifications commencing ∼10−7 mya.
A chromosome-scale reference genome for Giardia intestinalis WB
Publisher: Springer Science and Business Media LLC
Date: 04-02-2020
DOI: 10.1038/S41597-020-0377-Y
Abstract: Giardia intestinalis is a protist causing diarrhea in humans. The first G. intestinalis genome, from the WB isolate, was published more than ten years ago, and has been widely used as the reference genome for Giardia research. However, the genome is fragmented, thus hindering research at the chromosomal level. We re-sequenced the Giardia genome with Pacbio long-read sequencing technology and obtained a new reference genome, which was assembled into near-complete chromosomes with only four internal gaps at long repeats. This new genome is not only more complete but also better annotated at both structural and functional levels, providing more details about gene families, gene organizations and chromosomal structure. This near-complete reference genome will be a valuable resource for the Giardia community and protist research. It also showcases how a fragmented genome can be improved with long-read sequencing technology completed with optical maps.
Impact of gastrointestinal parasitic nematodes of sheep, and the role of advanced molecular tools for exploring epidemiology and drug resistance - an Australian perspective
Publisher: Springer Science and Business Media LLC
Date: 27-05-2013
Evolutionary epidemiology of a zoonosis
Publisher: Cold Spring Harbor Laboratory
Date: 16-10-2021
DOI: 10.1101/2021.10.15.464618
Abstract: Cryptosporidium parvum is a global zoonoses and a major cause of diarrhoea in humans and ruminants. The parasite’s life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture (3) there have been multiple genetic exchanges, and all are likely recent (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide ersity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalisation and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race. All raw and processed sequencing data generated and analysed during the current study have been submitted to the NCBI Sequence Read Archive ( ioproject/ ), under BioProjects PRJNA634014 and PRJNA633764.
Direct nanopore sequencing of mrna reveals landscape of transcript isoforms in apicomplexan parasites
Publisher: American Society for Microbiology
Date: 27-04-2021
DOI: 10.1128/MSYSTEMS.01081-20
Abstract: We have used a novel nanopore sequencing technology to directly analyze parasite transcriptomes. The very long reads of this technology reveal the full-length genes of the parasites that cause malaria and toxoplasmosis. Gene transcripts must be processed in a process called splicing before they can be translated to protein. Our analysis reveals that these parasites very frequently only partially process their gene products, in a manner that departs dramatically from their human hosts.
Passive Sampling of SARS-CoV-2 for Wastewater Surveillance
Publisher: American Chemical Society (ACS)
Date: 15-07-2021
First genetic analysis of Cryptosporidium from humans from Tasmania, and identification of a new genotype from a traveller to Bali
Publisher: Wiley
Date: 28-07-2014
Abstract: Little is known about the molecular composition of Cryptosporidium species from humans living in the insular state of Tasmania, Australia. In the present study, we genetically characterized 82 s les of Cryptosporidium from humans following conventional coproscopic testing in a routine, diagnostic laboratory. Using a PCR-coupled single-strand conformation polymorphism (SSCP) technique, targeting portions of the small subunit rRNA (SSU), and 60 kDa glycoprotein (gp60) loci, we identified two species of Cryptosporidium, including C. hominis (subgenotypes IbA10G2, IdA16, IeA12G3T3, and IfA19G1) and C. parvum (IIaA16G1R1 and IIaA18G3), and a new operational taxonomic unit (OTU) that genetically closely resembled C. wrairi. This OTU was further characterized using markers in the actin, Cryptosporidium oocyst wall protein (COWP), and 70 kDa heat shock protein (hsp70) genes. This study provides the first characterization of species and genotypes of Cryptosporidium from Tasmania, and presents clear genetic evidence, using five independent genetic loci, for a new genotype or species of Cryptosporidium in a Tasmanian person with a recent history of travelling to Bali, Indonesia. It would be interesting to undertake detailed molecular-based studies of Cryptosporidium in Indonesia and neighbouring countries, in conjunction with morphological and experimental investigations of new genotypes.
Insights into the immuno-molecular biology of Angiostrongylus vasorum through transcriptomics-Prospects for new interventions
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.BIOTECHADV.2013.07.006
Abstract: Angiostrongylus vasorum is a metastrongyloid nematode of dogs and other canids of major clinical importance in many countries. In order to gain first insights into the molecular biology of this worm, we conducted the first large-scale exploration of its transcriptome, and predicted essential molecules linked to metabolic and biological processes as well as host immune responses. We also predicted and prioritized drug targets and drug candidates. Following Illumina sequencing (RNA-seq), 52.3 million sequence reads representing adult A. vasorum were assembled and annotated. The assembly yielded 20,033 contigs, which encoded proteins with 11,505 homologues in Caenorhabditis elegans, and additional 2252 homologues in various other parasitic helminths for which curated data sets were publicly available. Functional annotation was achieved for 11,752 (58.6%) proteins predicted for A. vasorum, including peptidases (4.5%) and peptidase inhibitors (1.6%), protein kinases (1.7%), G protein-coupled receptors (GPCRs) (1.5%) and phosphatases (1.2%). Contigs encoding excretory/secretory and immuno-modulatory proteins represented some of the most highly transcribed molecules, and encoded enzymes that digest haemoglobin were conserved between A. vasorum and other blood-feeding nematodes. Using an essentiality-based approach, drug targets, including neurotransmitter receptors, an important chemosensory ion channel and cysteine proteinase-3 were predicted in A. vasorum, as were associated small molecular inhibitors/activators. Future transcriptomic analyses of all developmental stages of A. vasorum should facilitate deep explorations of the molecular biology of this important parasitic nematode and support the sequencing of its genome. These advances will provide a foundation for exploring immuno-molecular aspects of angiostrongylosis and have the potential to underpin the discovery of new methods of intervention.
Comparative evaluation of two DNA isolation techniques for PCR-based diagnosis of gastrointestinal nematode infections in sheep
Publisher: Elsevier BV
Date: 06-2013
DOI: 10.1016/J.MCP.2013.03.002
Abstract: The specific diagnosis of gastrointestinal parasite infections in livestock is central to their control. PCR assays have been developed for routine diagnosis and to overcome limitations of classical methods. Central to the performance of such assays is the effective isolation of the nucleic acids from s les and the elimination of components that are inhibitory to PCR. Here, we directly compared two techniques for the isolation of DNA from strongylid nematode eggs from faecal s les from sheep, and assessed their performance in relation to the sensitivity and specificity of PCR, time required for DNA isolation and ease of use. The results showed differences in the performance of the two isolation techniques, subsequently effecting the PCR results. The main differences related to the time required for DNA isolation, and the elimination of inhibitory substances from the DNA isolated by one technique but not the other.
Annotation of the Giardia proteome through structure-based homology and machine learning
Publisher: Oxford University Press (OUP)
Date: 06-12-2018
Single-cell RNA sequencing ofPlasmodiumvivax sporozoites reveals stage- and species-specific transcriptomic signatures
Publisher: Cold Spring Harbor Laboratory
Date: 24-11-2021
DOI: 10.1101/2021.11.24.469176
Abstract: Plasmodium vivax sporozoites reside in the salivary glands of a mosquito before infecting a human host. Previous transcriptome-wide studies in populations of these forms were limited in their ability to elucidate cell-to-cell variation, thereby masking cellular states potentially important in understanding transmission outcomes. In this study, we performed transcription profiling on 9,947 P. vivax sporozoites to assess the extent to which they differ at single-cell resolution. We show that sporozoites residing in the mosquito’s salivary glands exist in distinct developmental states, as defined by their transcriptomic signatures. Additionally, relative to P. falciparum, P. vivax displays overlapping and unique gene usage patterns, highlighting conserved and species-specific gene programs. Notably, distinguishing P. vivax from P. falciparum were a subset of P. vivax sporozoites expressing genes associated with translational regulation and repression. Finally, our comparison of single-cell transcriptomic data from P. vivax sporozoite and erythrocytic forms reveals gene usage patterns unique to sporozoites. In defining the transcriptomic signatures of in idual P. vivax sporozoites, our work provides new insights into the factors driving their developmental trajectory and lays the groundwork for a more comprehensive P. vivax cell atlas.
Generation of programmable dynamic flow patterns in microfluidics using audio signals.
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1LC00568E
Abstract: Customised audio signals, such as musical notes, can be readily generated by audio software on smartphones and played over audio speakers. Audio speakers translate electrical signals into the mechanical motion of the speaker cone. Coupling the inlet tube to the speaker cone causes the harmonic oscillation of the tube, which in turn changes the velocity profile and flow rate. We employ this strategy for generating programmable dynamic flow patterns in microfluidics. We show the generation of customised rib and vortex patterns through the application of multi-tone audio signals in water-based and whole blood s les. We demonstrate the precise capability to control the number and extent of the ribs and vortices by simply setting the frequency ratio of two- and three-tone audio signals. We exemplify potential applications of tube oscillation for studying the functional responses of circulating immune cells under pathophysiological shear rates. The system is programmable, compact, low-cost, biocompatible, and durable. These features make it suitable for a variety of applications across chemistry, biology, and physics.
Extracellular vesicles from early stage Plasmodium falciparum-infected red blood cells contain PfEMP1 and induce transcriptional changes in human monocytes
Publisher: Hindawi Limited
Date: 15-02-2018
DOI: 10.1111/CMI.12822
Abstract: Pathogens can release extracellular vesicles (EVs) for cell-cell communication and host modulation. EVs from Plasmodium falciparum, the deadliest malaria parasite species, can transfer drug resistance genes between parasites. EVs from late-stage parasite-infected RBC (iRBC-EVs) are immunostimulatory and affect endothelial cell permeability, but little is known about EVs from early stage iRBC. We detected the parasite virulence factor PfEMP1, which is responsible for iRBC adherence and a major contributor to disease severity, in EVs, only up to 12-hr post-RBC invasion. Furthermore, using PfEMP1 transport knockout parasites, we determined that EVs originated from inside the iRBC rather than the iRBC surface. Proteomic analysis detected 101 parasite and 178 human proteins in iRBC-EVs. Primary human monocytes stimulated with iRBC-EVs released low levels of inflammatory cytokines and showed transcriptomic changes. Stimulation with iRBC-EVs from PfEMP1 knockout parasites induced more gene expression changes and affected pathways involved in defence response, stress response, and response to cytokines, suggesting a novel function of PfEMP1 when present in EVs. We show for the first time the presence of PfEMP1 in early stage P. falciparum iRBC-EVs and the effects of these EVs on primary human monocytes, uncovering a new mechanism of potential parasite pathogenesis and host interaction.
The evolution of intramitochondriality in Midichloria bacteria
Publisher: Wiley
Date: 12-06-2023
Abstract: Midichloria spp. are intracellular bacterial symbionts of ticks. Representatives of this genus colonise mitochondria in the cells of their hosts. To shed light on this unique interaction we evaluated the presence of an intramitochondrial localization for three Midichloria in the respective tick host species and generated eight high‐quality draft genomes and one closed genome, showing that this trait is non‐monophyletic, either due to losses or multiple acquisitions. Comparative genomics supports the first hypothesis, as the genomes of non‐mitochondrial symbionts are reduced subsets of those capable of colonising the organelles. We detect genomic signatures of mitochondrial tropism, including the differential presence of type IV secretion system and flagellum, which could allow the secretion of unique effectors and/or direct interaction with mitochondria. Other genes, including adhesion molecules, proteins involved in actin polymerisation, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, to fuse with the organelles or manipulate the mitochondrial network.
3, 2, 1, go! Cryptosporidium counts down to sex
Publisher: Public Library of Science (PLoS)
Date: 12-05-2022
Evaluation and application of a molecular method to assess the composition of strongylid nematode populations in sheep with naturally acquired infections
Publisher: Elsevier BV
Date: 07-2011
DOI: 10.1016/J.MEEGID.2011.01.013
Abstract: We evaluated the performance of a PCR method for the diagnosis of naturally acquired strongylid nematode infections in sheep (n = 470 in a temperate climatic zone of south-eastern Australia), using a panel of 100 'negative control' s les from sheep known not to harbour parasitic helminths. We compared the diagnostic sensitivity (98%) and specificity (100%) of this assay against a conventional faecal flotation method and also established a system to rank the contribution of particular strongylid nematodes to the faecal egg counts (FECs) from 'mixed infections' in in idual sheep. The testing of faecal s les herein revealed that Teladorsagia circumcincta (80%) and Trichostrongylus spp. (66%) were most prevalent, followed by Chabertia ovina (33%), Oesophagostomum venulosum (28%) and Haemonchus contortus (1%). For the majority of sheep in this study, T. circumcincta and Trichostrongylus spp. represented the largest proportion of strongylid eggs in faecal s les from in idual sheep. This is the first large-scale prevalence survey of gastrointestinal nematodes in live sheep using a molecular tool. The ability to rapidly rank strongylid nematodes according to their contribution to mixed infections represents a major advantage over routine coprological methods. This PCR tool has the potential to replace the conventional technique of larval culture. Future efforts will focus on enhancing and adapting this molecular method for high throughput application in routine, diagnostic settings.
“MT-PCR – A rapid, reliable and effective tool for assessing toxic ‘algal’ blooms in Victorian water supplies: aiding protection and preservation”
Publisher: IWA Publishing
Date: 05-2015
Toward next-generation sequencing of mitochondrial genomes — Focus on parasitic worms of animals and biotechnological implications
Publisher: Elsevier BV
Date: 2010
DOI: 10.1016/J.BIOTECHADV.2009.11.002
Abstract: Helminths (worms) include parasitic nematodes (roundworms) and platyhelminths (flatworms). These worms are abundant, and many of them are of agricultural, aquacultural, veterinary and medical importance and cause substantial socioeconomic losses worldwide. The genetic characterization of parasitic nematodes using advanced molecular tools is central to the diagnosis of infections and the control of parasitism. The accurate analysis of genetic variation also underpins studies of their taxonomy, epidemiology and evolutionary history. Although the nuclear genome contains suitable genetic markers (e.g., in ribosomal DNA) for the identification of many species, the large size and high variability of the mt genome consistently provides a rich source of such markers for informative systematic and epidemiological studies both within and among species. There is significant value in establishing a practical platform for the rapid sequencing, annotation and analysis of mt genomic datasets to underpin such fundamental and applied studies of parasitic worms (= helminths). In the last decade, there have been some important advances in the mt genomics of helminths, but next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation. In this article, we provide a background on mt genomics, cover technological challenges and recent advances, and provide a perspective on future mt genome research of parasitic helminths and its fundamental scientific and biotechnological implications.
Proteomic Analysis of the Excretory-Secretory Products from Larval Stages of Ascaris suum Reveals High Abundance of Glycosyl Hydrolases
Publisher: Public Library of Science (PLoS)
Date: 03-10-2013
Genetic blueprint of the zoonotic pathogen Toxocara canis
Publisher: Springer Science and Business Media LLC
Date: 04-02-2015
DOI: 10.1038/NCOMMS7145
Eukaryote-conserved histone post-translational modification landscape in Giardia duodenalis revealed by mass spectrometry
Publisher: Elsevier BV
Date: 03-2021
A Real-Time PCR Assay for the Diagnosis of Gastrointestinal Nematode Infections of Small Ruminants
Publisher: Springer New York
Date: 28-10-2014
DOI: 10.1007/978-1-4939-2004-4_10
Abstract: The diagnosis of gastrointestinal nematode infections in small ruminants is central to studying the biology and epidemiology of these parasites and underpins their control. Traditional methods of diagnosis are inaccurate, time-consuming and laborious. Here, we describe a step-by-step protocol for the molecular-based diagnosis of infections by real-time PCR.
American variants of Cryptosporidium hominis: Over-sexed and over here?
Publisher: Elsevier BV
Date: 2023
Massively Parallel Sequencing and Analysis of the Necator americanus Transcriptome
Publisher: Public Library of Science (PLoS)
Date: 11-05-2010
New Thelastomatoidea (Nematoda: Oxyurida) from Australian burrowing cockroaches (Blaberidae: Geoscapheinae, Panesthiinae)
Publisher: Brill
Date: 2006
DOI: 10.1163/156854106778493484
Abstract: Four new species and two new genera of thelastomatoid are described from several species of Australian burrowing cockroaches (Blattodea: Panesthiinae Geoscapheinae). Corpicracens munozae n. g., n. sp., Pseudodesmicola botti n. g., n. sp. and Cephalobellus nolani n. sp. are described from Geoscapheus dilatatus (Blattodea: Geoscapheinae) from Mendooran, New South Wales one new thelastomatid, Blattophila praelongicauda n. sp., is described from Panesthia cribrata from Lamington National Park, Queensland. Corpicracens munozae n. g., n. sp. is long and slender, with a monodelphic female reproductive system, a clavate corpus with a slight posterior pseudobulb, oval eggs flattened at the poles, and a relatively robust, subulate tail. Pseudodesmicola botti n. g., n. sp. is slightly more robust in body, also has a monodelphic reproductive system, a cylindrical corpus with a posterior pseudobulb, ovoid eggs and a very long, subulate tail. Cephalobellus nolani n. sp. is distinguished from other members of the genus by its relatively short and broad body and egg shape. Lastly, Blattophila praelongicauda n. sp. is distinguished from other members of the genus by having eggs with a single, polar operculum, tail length, and position of the vulva, nerve ring and excretory pore. An additional species, known by a single specimen from Panesthia tryoni tryoni from the same locality is characterised but not named. The species found are all relatively rare parasites of Australian burrowing cockroaches, each having a prevalence of less than 10%.
Transcriptome and histone epigenome ofPlasmodium vivaxsalivary-gland sporozoites point to tight regulatory control and potential mechanisms for liver-stage differentiation
Publisher: Cold Spring Harbor Laboratory
Date: 07-06-2017
DOI: 10.1101/145250
Abstract: Plasmodium vivax is the key obstacle to malaria elimination in Asia and Latin America, largely attributed to its ability to form resilient hypnozoites (sleeper-cells) in the host liver that escape treatment and cause relapsing infections. The decision to form hypnozoites is made early in the liver infection and may already be set in sporozoites prior to invasion. To better understand these early stages of infection, we undertook a comprehensive transcriptomic and histone epigenetic characterization of P. vivax sporozoites. The salivary-gland sporozoite transcriptome is heavily composed of transcripts associated with functions needed for early infection of the vertebrate host and development within hepatocytes. Through comparisons to recently published proteome data for the P. vivax sporozoite, our study finds that although highly transcribed, these transcripts are not detectable as proteins and may be regulated through translational repression a finding we test for a small subset of transcripts and proteins through immunofluorescent microscopy of sporozoites and liver stages in humanized mice. We identify differential transcription between the sporozoite and published transcriptomes of asexual blood-stages and mixed versus hypnozoite-enriched liver stages. These comparisons point to multiple layers of transcriptional, post-transcriptional and post-translational control that appear active in sporozoites and to a lesser extent hypnozoites, but largely absent in replicating liver schizonts or mixed blood-stages. Common transcripts up-regulated in sporozoites and hypnozoites compared to mixed (i.e., schizont) liver-stages identify genes linked to dormancy ersistence in bacteria, amoebae and plants. We also characterise histone epigenetic modifications in the P. vivax sporozoite and explore their role in regulating transcription. Collectively, these data support the hypothesis that the sporozoite as a tightly programmed stage primed to infect the human host and identifies potential mechanisms for hypnozoite-formation that may be further explored in liver stage models.
Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets
Publisher: Cold Spring Harbor Laboratory
Date: 02-2022
DOI: 10.1101/2022.02.01.478648
Abstract: The resilience of Plasmodium vivax , the most widely distributed malaria-causing parasite in humans, is attributed to its ability to produce dormant liver forms known as hypnozoites, which can activate weeks, months, or even years after an initial mosquito bite. The factors underlying hypnozoite formation and activation are poorly understood, as is the parasite’s influence on the host hepatocyte. Here, we shed light on transcriptome-wide signatures of both the parasite and the infected host cell by sequencing over 1,000 P. vivax -infected hepatocytes at single-cell resolution. We distinguish between replicating schizonts and hypnozoites at the transcriptional level, identifying key differences in transcripts encoding for RNA-binding proteins associated with cell fate. In infected hepatocytes, we show that genes associated with energy metabolism and antioxidant stress response were upregulated, and those involved in the host immune response downregulated, suggesting both schizonts and hypnozoites alter the host intracellular environment. The transcriptional markers in schizonts, hypnozoites, and infected hepatocytes revealed here pinpoint potential factors underlying dormancy and can inform therapeutic targets against P. vivax liver-stage infection.
Differential protein expression and post-translational modifications in metronidazole-resistant Giardia duodenalis
Publisher: Oxford University Press (OUP)
Date: 13-03-2018
A comprehensive analysis of the biogeography of the thelastomatoid pinworms from Australian burrowing cockroaches (Blaberidae: Geoscapheinae, Panesthiinae): no evidence of coevolution
Publisher: Cambridge University Press (CUP)
Date: 24-04-2007
DOI: 10.1017/S0031182007002843
Abstract: We report 21 thelastomatoid species parasitizing 31 described and 5 undescribed geoscapheine and panesthiine cockroaches, representing all but 1 of the known species of these subfamilies in Australia. The nematodes have 3 distinct patterns of host distribution: dominant, moderate and rare. The 4 dominant species, Cordonicola gibsoni , Leidynemella fusiformis , Travassosinema jaidenae and Aoruroides queenslandensis , are highly prevalent, found in nearly all host species examined, and broadly distributed. The 8 moderate species have lower prevalences but are still widely distributed. Many of these species are more common in one host subfamily than the other. The remaining 9 rare species have highly restricted host and geographical distributions. Six of the 21 species are exclusive to geoscapheines, 5 to panesthiines and 10 are shared. These patterns suggest that most of the reported thelastomatoid species are generalists rather than specialists, that host-specificity within this group is low and that co-evolutionary speciation has had little, if any, impact on structuring the thelastomatoid fauna of Australian burrowing cockroaches. In a broader context, this study provides the first comprehensive examination of the role of coevolutionary speciation and host specificity in regulating the distribution of pinworms in arthropods.
First molecular characterisation of Cryptosporidium and Giardia from Bubalus bubalis (water buffalo) in Victoria, Australia
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.MEEGID.2013.07.019
Abstract: We conducted a molecular epidemiological survey of Cryptosporidium and Giardia from Bubalus bubalis (water buffalo) on two extensive farms (450 km apart) in Victoria, Australia. Faecal s les (n=476) were collected from different age groups of water buffalo at two time points (six months apart) and tested using a PCR-based mutation scanning-targeted sequencing-phylogenetic approach, employing markers within the small subunit of ribosomal RNA (designated pSSU) and triose phosphate isomerase (ptpi) genes. Based on pSSU data, Cryptosporidium parvum, Cryptosporidium bovis and Cryptosporidium genotypes 1, 2 (each 99% similar genetically to Cryptosporidium ryanae) and 3 (99% similar to Cryptosporidium suis) were detected in two (0.4%), one (0.2%), 38 (8.0%), 16 (3.4%) and one (0.2%) of the 476 s les tested, respectively. Using ptpi, Giardia duodenalis assemblages A and E were detected in totals of 56 (11.8%) and six (1.3%) of these s les, respectively. Cryptosporidium was detected on both farms, whereas Giardia was detected only on farm B, and both genera were detected in 1.5% of all s les tested. The study showed that water buffaloes on these farms excreted C. parvum and/or G. duodenalis assemblage A, which are consistent with those found in humans, inferring that these particular pathogens are of zoonotic significance. Future work should focus on investigating, in a temporal and spatial manner, the prevalence and intensity of such infections in water buffaloes in various geographical regions in Australia and in other countries.
Cryptosporidium: Current State of Genomics and Systems Biological Research
Publisher: Springer Vienna
Date: 14-09-2013
A thermo‐resistant and RNase‐sensitive cargo from Giardia duodenalis extracellular vesicles modifies the behaviour of enterobacteria
Publisher: Wiley
Date: 30-08-2023
DOI: 10.1002/JEX2.109
Abstract: Extracellular vesicles (EVs) recently emerged as important players in the pathophysiology of parasitic infections. While the protist parasite Giardia duodenalis can produce EVs, their role in giardiasis remains obscure. Giardia can disrupt gut microbiota biofilms and transform commensal bacteria into invasive pathobionts at sites devoid of colonizing trophozoites via unknown mechanisms. We hypothesized that Giardia EVs could modify gut bacterial behaviour via a novel mode of trans‐kingdom communication. Our findings indicate that Giardia EVs exert bacteriostatic effects on Escherichia coli HB101 and Enterobacter cloacae TW1, increasing their swimming motility. Giardia EVs also decreased the biofilm‐forming ability of E. coli HB101 but not by E. cloacae TW1, supporting the hypothesis that these effects are, at least in part, bacteria‐selective. E. coli HB101 and E. cloacae TW1 exhibited increased adhesion/invasion onto small intestine epithelial cells when exposed to Giardia EVs. EVs labelled with PKH67 revealed colocalization with E. coli HB101 and E. cloacae TW1 bacterial cells. Small RNA sequencing revealed a high abundance of ribosomal RNA (rRNA)‐ and transfer RNA (tRNA)‐derived small RNAs, short‐interfering RNAs (siRNAs) and micro‐RNAs (miRNAs) within Giardia EVs. Proteomic analysis of EVs uncovered the presence of RNA chaperones and heat shock proteins that can facilitate the thermal stability of EVs and its sRNA cargo, as well as protein‐modifying enzymes. In vitro, RNase heat‐treatment assays showed that total RNAs in EVs, but not proteins, are responsible for modulating bacterial swimming motility and biofilm formation. G. duodenalis small RNAs of EVs, but not proteins, were responsible for the increased bacterial adhesion to intestinal epithelial cells induced upon exposure to Giardia EVs. Together, the findings indicate that Giardia EVs contain a heat‐stable, RNase‐sensitive cargo that can trigger the development of pathobiont characteristics in Enterobacteria, depicting a novel trans‐kingdom cross‐talk in the gut.
Harnessing Genomic Technologies to Explore the Molecular Biology of Liver Flukes-Major Implications for Fundamental and Applied Research
Publisher: Wiley
Date: 18-07-2012
The Transcriptome of Trichuris suis - First Molecular Insights into a Parasite with Curative Properties for Key Immune Diseases of Humans
Publisher: Public Library of Science (PLoS)
Date: 24-08-2011
Local climate aridity influences the distribution of thelastomatoid nematodes of the Australian giant burrowing cockroach
Publisher: Cambridge University Press (CUP)
Date: 20-04-2007
DOI: 10.1017/S0031182007002727
Abstract: In this study, we examined the effects of local climate aridity on the richness and composition of the thelastomatoid (Nematoda: Oxyurida) guild parasitizing the Australian giant burrowing cockroach, Macropanesthia rhinoceros (Blattodea: Geoscapheinae). In total, 9 thelastomatoid species parasitized this cockroach in north-eastern Australia (Queensland). Local observed richness ranged from 3 species (in Cooktown, Magnetic Island, Maiden Springs and Whitsunday Island) to 7 species (in Rochford Scrub). The lowest richness occurred in both relatively wet and dry climates, and the highest richness was in moderate climates. Three species, Cordonicola gibsoni , Leidynemella fusiformis and Travassosinema jaidenae , were found at all 13 collection sites. One species, Geoscaphenema megaovum , was found exclusively in dry to moderate climates. The remaining species, Blattophila sphaerolaima , Coronostoma australiae , Desmicola ornata , Hammerschmidtiella hochi and Jaidenema rhinoceratum , were found in moderate climates only. We hypothesize that the egg is the stage in the thelastomatoid life-cycle most vulnerable to the effects of adverse climate and that the geographical distribution for each species is, in part, bound by environments that are too dry, resulting in egg desiccation, and by environments that are too wet, resulting in decreased oxygen uptake across the egg-shell and in osmotic lysing.
Recent Progress in Transcriptomics of Key Gastrointestinal Nematodes of Animals - Fundamental Research Toward New Intervention Strategies
Publisher: Wiley
Date: 18-07-2012
Proteomic diversity in a prevalent human-infective Giardia duodenalis sub-species
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.IJPARA.2018.05.003
Abstract: Giardia duodenalis a species complex of gastrointestinal protists, with assemblages A and B infective to humans. To date, post-genomic proteomics are largely derived from Assemblage A, biasing understanding of parasite biology. To address this gap, we quantitatively analysed the proteomes of trophozoites from the genome reference and two clinical Assemblage B isolates, revealing lower spectrum-to-peptide matches in non-reference isolates, resulting in significant losses in peptide and protein identifications, and indicating significant intra-assemblage variation. We also explored differential protein expression between in vitro cultured subpopulations putatively enriched for iding and feeding cells, respectively. This data is an important proteomic baseline for Assemblage B, highlighting proteomic differences between physiological states, and unique differences relative to Assemblage A.
Effective low-cost preservation of human stools in field-based studies for helminth and microbiota analysis
Publisher: Elsevier BV
Date: 03-2021
Multimodal regulation of encystation in Giardia duodenalis revealed by deep proteomics
Publisher: Elsevier BV
Date: 09-2021
Drug susceptibility testing for oxygen-dependent and oxygen-independent resistance phenotypes in trichomonads
Publisher: Elsevier BV
Date: 05-2023
Genetic characterization of Cryptosporidium parvum from calves by mutation scanning and targeted sequencing - zoonotic implications.
Publisher: Wiley
Date: 08-2009
Abstract: This study explored the genetic make-up of Cryptosporidium in fecal s les from 268 in idual calves on pasture-based dairy farms in three regions of Victoria, Australia. An integrated approach, using PCR-coupled single-strand conformation polymorphism, targeted sequencing and phylogenetic analysis, was employed to classify the genetic variants (i.e. genotypes and subgenotypes) of Cryptosporidium parvum present in 124 (46.3%) s les and to infer their zoonotic potential. Genotypic and subgenotypic classification was achieved using a portion of the 60 kDa glycoprotein gene (designated pgp60) specific identity was verified using a region within the small subunit of the nuclear ribosomal RNA (pSSU). Twelve sequence types representing ten distinct subgenotypes were defined within genotype IIa, namely IIaA16G3R1 (n=7), IIaA17G2R1 (1), IIaA18G2R1a (2), IIaA18G2R1b (1), IIaA18G4R1 (1), IIaA19G3R1a (80), IIaA19G3R1b (1), IIaA20G2R1 (9), IIaA20G3R1 (1), IIaA20G4R1 (9), IIaA21G3R1 (1) and IIaA23G3R1 (9), of which IIaA18G2R1b, IIaA18G4R1 and IIaA19G3R1b are new records. All of the subgenotypes, except IIaA16G3R1, IIaA18G4R1 and IIaA20G4R1, have been detected previously in humans and are thus considered to be of zoonotic relevance. (Nucleotide sequences reported in this paper are available in the GenBank database under accession numbers FJ825018-FJ825029).
Divergent Transcriptional Responses to Physiological and Xenobiotic Stress in Giardia duodenalis
Publisher: American Society for Microbiology
Date: 10-2016
DOI: 10.1128/AAC.00977-16
Abstract: Understanding how parasites respond to stress can help to identify essential biological processes. Giardia duodenalis is a parasitic protist that infects the human gastrointestinal tract and causes 200 to 300 million cases of diarrhea annually. Metronidazole, a major antigiardial drug, is thought to cause oxidative damage within the infective trophozoite form. However, treatment efficacy is suboptimal, due partly to metronidazole-resistant infections. To elucidate conserved and stress-specific responses, we calibrated sublethal metronidazole, hydrogen peroxide, and thermal stresses to exert approximately equal pressure on trophozoite growth and compared transcriptional responses after 24 h of exposure. We identified 252 genes that were differentially transcribed in response to all three stressors, including glycolytic and DNA repair enzymes, a mitogen-activated protein (MAP) kinase, high-cysteine membrane proteins, flavin adenine dinucleotide (FAD) synthetase, and histone modification enzymes. Transcriptional responses appeared to erge according to physiological or xenobiotic stress. Downregulation of the antioxidant system and α-giardins was observed only under metronidazole-induced stress, whereas upregulation of GARP-like transcription factors and their subordinate genes was observed in response to hydrogen peroxide and thermal stressors. Limited evidence was found in support of stress-specific response elements upstream of differentially transcribed genes however, antisense derepression and differential regulation of RNA interference machinery suggest multiple epigenetic mechanisms of transcriptional control.
Mutation scanning-coupled tools for the analysis of genetic variation in Taenia and diagnosis - Status and prospects
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.MEEGID.2009.05.005
Abstract: Cestodes of the genus Taenia occur as adult tapeworms in the small intestine of carnivorous definitive hosts and are transmitted to particular mammalian intermediate hosts, in which they develop as fluid-filled larvae in tissues, causing the disease cysticercosis or coenuriasis. A number of species are of medical importance and/or cause losses to the meat and livestock industry mainly due to the condemnation of infected muscle and offal. The control of taeniid cestodes relies upon epidemiological data, including the precise identification and characterization of the causative agents. Traditional, phenetic techniques have limitations for specific diagnosis. Although there has been progress in the establishment of molecular tools, there has been relatively limited application of mutation scanning approaches to species of Taenia. In the present article, we briefly review key genetic markers used for the specific identification of taeniids and tools for the analysis of genetic variation within and among populations and the diagnosis of taeniasis and cysticercosis/coenuriasis. We also discuss the advantages and disadvantages of selected techniques and emphasize the benefits of utilizing mutation scanning-based approaches in achieving detailed insights into the population genetics and epidemiology of Taenia species.
First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach
Publisher: Elsevier BV
Date: 12-2010
A Perspective on cryptosporidium and giardia, with an emphasis on bovines and recent epidemiological findings
Publisher: Elsevier
Date: 2015
Responses of the differentiated intestinal epithelial cell line Caco-2 to infection with the giardia intestinalis GS isolate
Publisher: Frontiers Media SA
Date: 16-07-2018
Genome and transcriptome of the porcine whipworm Trichuris suis
Publisher: Springer Science and Business Media LLC
Date: 15-06-2014
DOI: 10.1038/NG.3012
Transcriptional analysis identifies key genes involved in metabolism, fibrosis/tissue repair and the immune response against Fasciola hepatica in sheep liver
Publisher: Springer Science and Business Media LLC
Date: 25-02-2015
Sequence diversity and evolution of a group of iflaviruses associated with ticks
Publisher: Springer Science and Business Media LLC
Date: 19-04-2021
DOI: 10.1007/S00705-021-05060-8
Abstract: We studied a group of tick-associated viruses with characteristics of members of the family Iflaviridae , a family of viruses frequently found in arthropods. Our aim was to gain insight into the evolutionary dynamics of this group of viruses, which may be linked to the biology of ticks. We explored assembled RNA-Seq data sets for different species of ticks. We identified members of five different iflavirus species, four of them novel, and discovered nine new genome sequences, including variants. Five variants represented a virus species associated with Ixodes ricinus . Unexpectedly, a sequence found in the Ixodes scapularis cell line ISE6 was nearly identical to the sequences of I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Analysing patterns of substitutions between these variants, we detected a strong excess of synonymous mutations, suggesting evolution under strong positive selection. The phylogenies of the viruses and of their tick hosts were not congruent, suggesting recurrent host changes across tick genera during their evolution. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.
Investigating public health impacts of deer in a protected drinking water supply watershed
Publisher: IWA Publishing
Date: 07-2008
DOI: 10.2166/WST.2008.632
Abstract: The World Health Organisation's (WHO) Water Safety Plans highlight the need for preventative risk management when managing water contamination risks. As part of this approach, a management framework incorporating multiple barriers is necessary and there is a need to validate those barriers through scientific evidence. This paper reports on a study undertaken to validate the effectiveness, in terms of pathogen numbers, of having protected watersheds. The study aimed to determine if the deer population in a protected watershed carried Cryptosporidium and whether or not it was human infectious. Deer faecal s les were collected from the protected watersheds over a 12 month period and analysed using a new method, developed as part of this project, for genotyping Cryptosporidium. Early results showed the presence of Cryptosporidium, but following a refinement in the method no human infectious Cryptosporidium was detected. The results give some confidence that having protected watersheds is an effective barrier against pathogen contamination. They do not, however, imply that continued monitoring and management of the deer should cease. To maintain compliance with the Water Safety Plans, continual validation of barrier effectiveness is required.
Global population genomics of two subspecies ofCryptosporidium hominisduring 500 years of evolution
Publisher: Cold Spring Harbor Laboratory
Date: 09-09-2021
DOI: 10.1101/2021.09.09.459610
Abstract: Cryptosporidiosis is a major global health problem and a primary cause of diarrhoea, particularly in young children in low- and middle-income countries (LMICs). The zoonotic Cryptosporidium parvum and anthroponotic C. hominis cause most human infections. Here, we present a comprehensive whole-genome study of C. hominis , comprising 114 isolates from 16 countries within five continents. We detect two lineages with distinct biology and demography, which erged circa 500 years ago. We consider these lineages two subspecies and propose the names C. hominis hominis and C. hominis aquapotentis ( gp60 subtype IbA10G2). In our study, C. h. hominis is almost exclusively represented by isolates from LMICs in Africa and Asia and appears to have undergone recent population contraction. In contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America and Oceania, and appears to be expanding. Notably, C. h. aquapotentis is associated with high rates of direct human-to-human transmission, which may explain its success in countries with well-developed environmental sanitation infrastructure. Intriguingly, we detected genomic regions of introgression following secondary contact between the subspecies. This resulted in high ersity and ergence in genomic islands of putative virulence genes (GIPVs), including muc5 (CHUDEA2_430) and a hypothetical protein (CHUDEA6_5270). This ersity is maintained by balancing selection, suggesting a coevolutionary arms race with the host. Lastly, we find that recent gene flow from C. h. aquapotentis to C. h. hominis , likely associated with increased human migration, may be driving evolution of more virulent C. hominis variants.
Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites
Publisher: Cold Spring Harbor Laboratory
Date: 17-02-2020
DOI: 10.1101/2020.02.16.946699
Abstract: Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterised in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been h ered by atypical transcriptomic features, such as the high AT content of Plasmodium RNA, but also the limitations of short read sequencing in deciphering complex splicing events. In this study, we utilised the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies (ONT) to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum . We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or near full-length transcripts with comparable quantification to Illumina sequencing. By comparing this data with available gene models, we find widespread alternative splicing, particular intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic ersity, rather than expanding proteomic ersity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This work highlights a strategy in using long read sequencing to understand splicing events at the whole transcript level, and has implications in future interpretation of RNA-seq studies.
Deep sequencing approach for investigating infectious agents causing fever.
Publisher: Springer Science and Business Media LLC
Date: 14-05-2016
Conservation, abundance, glycosylation profile, and localization of the TSP protein family in Cryptosporidium parvum
Publisher: Elsevier BV
Date: 03-2023
Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation
Publisher: Springer Science and Business Media LLC
Date: 12-2007
Abstract: The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations. Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR lification of target sequences, through to the gel-based separation of licons and scanning for mutations by SSCP (either by the analysis of radiolabeled licons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point mutations for licon sizes of up to 450-500 bp, and usually takes 1-2 days to carry out. This user-friendly, low-cost, potentially high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be applied to any gene of any organism.
Time-Dependent Transcriptional Changes in Axenic Giardia duodenalis Trophozoites
Publisher: Public Library of Science (PLoS)
Date: 04-12-2015
Bioinformatic analysis of abundant, gender-enriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow platform
Publisher: Elsevier BV
Date: 10-2009
DOI: 10.1016/J.MCP.2009.03.003
Abstract: Expressed sequence tag (EST) data representing transcripts with a high level of differential hybridization in suppressive-subtractive hybridization (SSH)-based microarray analysis between adult female and male Ascaris suum were subjected to detailed bioinformatic analysis. A total of 361 ESTs clustered into 209 sequences, of which 52 and 157 represented transcripts that were enriched in female and male A. suum, respectively. Thirty (57.7%) of the 'female' subset of 52 sequences had orthologues/homologues in other parasitic nematodes and/or Caenorhabditis elegans, 13 (25%) exclusively in other parasitic nematodes and nine (17.3%) had no match in any other organism for which sequence data are currently available the C. elegans orthologues encoded molecules involved in reproduction as well as embryonic and gamete development, such as vitellogenins and chitin-binding proteins. Of the 'male' subset of 157 sequences, 73 (46.5%) had orthologues/homologues in other parasitic nematodes and/or C. elegans, 57 (37.5%) in other parasitic nematodes only, and 22 (14.5%) had no significant similarity match in any other organism the C. elegans orthologues encoded predominantly major sperm proteins (MSPs), kinases and phosphatases, actins, myosins and an Ancylostoma secreted protein-like molecule. The findings of the present study should support further genomic investigations of A. suum.
Thelastomatoidea (Nematoda: Oxyurida) of the Australian giant burrowing cockroach, Macropanesthia rhinoceros (Blaberidae: Geoscapheinae)
Publisher: Brill
Date: 2006
DOI: 10.1163/156854106778493501
Abstract: The thelastomatoid fauna of Macropanesthia rhinoceros was examined from 13 localities across its range in Queensland, Australia. Nine species of thelastomatoids, including two representing new genera, Geoscaphenema megaovum n. g., n. sp. and Jaidenema rhinoceratum n. g., n. sp., were found. Macropanesthia rhinoceros is reported as a new host for seven species previously recorded from Panesthia cribrata (Blaberidae: Panesthiinae) and P. tryoni tryoni, viz, Blattophila sphaerolaima, Leidynemella fusiformis, Cordonicola gibsoni, Travassosinema jaidenae, Coronostoma australiae, Hammerschmidtiella hochi and Desmicola ornata. Overall estimated richness for the system ranged from 10.1-13.5 species. The high degree of parasite faunal overlap between M. rhinoceros and the two Panesthia species is surprising given the disparate ecological niches that they occupy P. cribrata and P. tryoni tryoni burrow in, and feed upon, moist decaying wood and require a climate that is moist all year round, whereas M. rhinoceros burrows in loose soil, feeds on fallen leaf litter and is tolerant of much drier environments.
Recent advances in functional research in Giardia intestinalis
Publisher: Elsevier
Date: 2020
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets
Publisher: Springer Science and Business Media LLC
Date: 04-12-2015
DOI: 10.1038/SREP17759
Abstract: The blood fluke Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease (NTD) that affects more than 110 million people. Treating this disease by targeted or mass administration with a single chemical, praziquantel, carries the risk that drug resistance will develop in this pathogen. Therefore, there is an imperative to search for new drug targets in S. haematobium and other schistosomes. In this regard, protein kinases have potential, given their essential roles in biological processes and as targets for drugs already approved by the US Food and Drug Administration (FDA) for use in humans. In this context, we defined here the kinome of S. haematobium using a refined bioinformatic pipeline. We classified, curated and annotated predicted kinases and assessed the developmental transcription profiles of kinase genes. Then, we prioritised a panel of kinases as potential drug targets and inferred chemicals that bind to them using an integrated bioinformatic pipeline. Most kinases of S. haematobium are very similar to those of its congener, S. mansoni , offering the prospect of designing chemicals that kill both species. Overall, this study provides a global insight into the kinome of S. haematobium and should assist the repurposing or discovery of drugs against schistosomiasis.
Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda)
Publisher: Springer Science and Business Media LLC
Date: 2008
Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia
Publisher: Cold Spring Harbor Laboratory
Date: 02-02-2022
Abstract: During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the 3′ UTR of an mRNA, thus determining much of its post-transcriptional fate. Using long-read sequencing, we characterize the polyadenylation signal and related sequences surrounding Giardia lamblia cleavage sites for over 2600 genes. We find that G. lamblia uses an AGURAA poly(A) signal, which differs from the mammalian AAUAAA. We also describe how G. lamblia lacks common auxiliary elements found in other eukaryotes, along with the proteins that recognize them. Further, we identify 133 genes with evidence of alternative polyadenylation. These results suggest that despite pared-down cleavage and polyadenylation machinery, 3′ end formation still appears to be an important regulatory step for gene expression in G. lamblia .
Artificial intelligence takes center stage: exploring the capabilities and implications of ChatGPT and other AI-assisted technologies in scientific research and education
Publisher: Wiley
Date: 18-09-2023
DOI: 10.1111/IMCB.12689
Molecular detection of Cryptosporidium cuniculus in rabbits in Australia
Publisher: Elsevier BV
Date: 12-2010
DOI: 10.1016/J.MEEGID.2010.07.020
Abstract: In the United Kingdom, rabbits have been reported to harbour genotypes of Cryptosporidium (now recognized as C. cuniculus) identical to those from human patients exhibiting symptoms of cryptosporidiosis. The high density of rabbits in many regions of Australia, including both rural and urban as well as natural water catchments areas, and the absence of any information on Cryptosporidium from lagomorphs in this country stimulated the present study. We undertook an epidemiological study that genetically characterized Cryptosporidium from rabbits from four locations in Victoria by PCR-coupled sequencing and phylogenetic analysis of sequence data for loci within the small subunit of nuclear ribosomal RNA (SSU for specific identification) and the 60kDa glycoprotein gene (gp60 for genotypic/subgenotypic identification). Cryptosporidium was detected in 12 (6.8%) of 176 in idual faecal s les. For SSU, all 12 sequences were identical to each other and to that of C. cuniculus. For pgp60, all corresponding sequences matched the known genotype Vb, and were classified as subgenotype VbA23R3 (n=11) and VbA26R4 (n=1), which are both new records. Present evidence indicates that genotype Vb is limited to rabbits however, it would be premature to conclude that this genotype is not zoonotic. Future studies should focus on the zoonotic potential of C. cuniculus from rabbits and a wide range of yet unstudied animals. (Nucleotide sequences reported in this paper are available in the GenBank database under accession nos. HM852431-HM852433).
A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing
Publisher: Oxford University Press (OUP)
Date: 03-08-2010
DOI: 10.1093/NAR/GKQ667
A communal catalogue reveals Earth’s multiscale microbial diversity
Publisher: Springer Science and Business Media LLC
Date: 11-2017
DOI: 10.1038/NATURE24621
Abstract: Our growing awareness of the microbial world’s importance and ersity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community s les collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of ersity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial ersity.
A Molecular Diagnostic Tool to Replace Larval Culture in Conventional Faecal Egg Count Reduction Testing in Sheep
Publisher: Public Library of Science (PLoS)
Date: 22-05-2012
Time-course study of the transcriptome of peripheral blood mononuclear cells (PBMCs) from sheep infected with Fasciola hepatica
Publisher: Public Library of Science (PLoS)
Date: 20-07-2016
Cryptic Parasite Revealed. Improved Prospects for Treatment and Control of Human Cryptosporidiosis Through Advanced Technologies {star operator}
Publisher: Elsevier
Date: 2011
Profiling circulating miRNAs in serum from pigs infected with the porcine whipworm, Trichuris suis
Publisher: Elsevier BV
Date: 06-2016
DOI: 10.1016/J.VETPAR.2016.03.025
Abstract: microRNAs (miRNAs) are recently discovered as key regulators of gene translation and are becoming increasingly recognized for their involvement in various diseases. This study investigates the miRNA profile in pig serum during the course of an infection with the gastrointestinal parasite, Trichuris suis. Of this panel, the expression of selected miRNAs in serum from T. suis infected and uninfected pigs were determined by quantitative real time PCR using Exiqon Human Panel assays at 0, 2, 4, 6, 8 and 10 weeks post first infection (wpi). One miRNA, ssc-let-7d-3p, was significantly up-regulated in infected pigs 8 wpi. Interestingly, ssc-let-7d-3p shows high complementary to tsu-let-7a, which is the most highly transcribed miRNA in T. suis. The let-7 family miRNAs have been shown to post-transcriptionally regulate the translation of the helminth-controlling cytokine, IL-13, in a murine model for asthma and we hypothesize possible interactions between these host- and parasite-derived miRNAs and their immunomodulating roles.
Transcriptomics indicates active and passive metronidazole resistance mechanisms in three seminal Giardia lines
Publisher: Frontiers Media SA
Date: 17-03-2017
Genome variation in nine co-occurring toxic Cylindrospermopsis raciborskii strains
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.HAL.2018.03.001
Abstract: Cyanobacteria form harmful algal blooms and are highly adapted to a range of habitats, in part due to their phenotype plasticity. This plasticity is partially the result of co-existence of multiple strains within a single population. The toxic cyanobacterium Cylindrospermopsis raciborskii has remarkable phenotypic plasticity, strain variation and environmental adaptation resulting in an expansion of its global range. To understand the genetic basis of the high level of plasticity within a C. raciborskii population, the genomes of nine co-occurring strains were compared. The strains differed in morphology, toxin cell quotas and physiology, despite being obtained from a single water s le. Comparative genomics showed that three coiled strains were 3.9 Mbp in size, with 3544 ± 11 genes, while straight strains were 3.8 Mbp in size, with 3485 ± 20 genes. The core proteome comprised 86% of the genome and consisted of 2891 orthologous groups (OGs), whereas the variable genome comprised ∼14% (847 OGs), and the strain specific genome only ∼1% (433 OGs).There was a high proportion of variable strain-specific genes for the very closely related strains, which may underpin strain differentiation. The variable genes were associated with environmental responses and adaptation, particularly phage defence, DNA repair, membrane transport, and stress, illustrative of the adaptability of the strains in response to environmental and biological stressors. This study shows that high genomic variability exists between co-occurring strains and may be the basis of strain phenotypic differences and plasticity of populations. Therefore management and prediction of blooms of this harmful species requires different approaches to capture this strain variability.
Circadian disruption of ICU patients: A review of pathways, expression, and interventions
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.JCRC.2016.12.006
Abstract: Intensive care unit patients typically exhibit pathologic wakefulness, poor quality of daytime sleep, nocturnal sleep fragmentation, and sleep patterns that feature the absence of slow wave sleep and rapid eye movement. This article offers a review of the existing literature examining circadian desynchronization in critically ill patients, highlighting contributing factors identified by scholars, and circadian abnormalities observed in these patients. It discusses potential implications for clinical practice and suggests avenues of future research. Elucidating the role of circadian rhythms in the management of critical illness can guide future chronotherapeutic approaches and optimize patient outcomes.
Establishment of a robotic, high-throughput platform for the specific diagnosis of gastrointestinal nematode infections in sheep
Publisher: Elsevier BV
Date: 12-2012
DOI: 10.1016/J.IJPARA.2012.10.005
Abstract: The accurate diagnosis of strongylid nematode infections is central to investigating their epidemiology and for parasite control. To overcome major limitations in sensitivity or specificity of traditional methods, including faecal egg count (FEC) and/or larval culture (LC), we evaluated and established a semi-automated, high throughput multiplexed-tandem PCR (MT-PCR) platform for the diagnosis of gastrointestinal strongylid nematode infections in sheep, and established its diagnostic sensitivity (100%) and specificity (87.5%) based on the testing of 100 faecal DNA s les from helminth-free sheep and 30 s les from sheep with infections confirmed by necropsy. Subsequently, the platform was employed to test 219 faecal s les from sheep with naturally acquired infections from various geographical localities within Australia and the results compared with those from conventional LC using 139 of the 219 s les. The results obtained using both MT-PCR and LC correlated significantly for most nematodes examined, but revealed that Oesophagostomum venulosum and Chabertia ovina (parasites of the large intestine) were significantly under-represented in the LC results. The results showed that Trichostrongylus spp. (87%), Teladorsagia circumcincta (80%) and Haemonchus contortus (67%) had the highest prevalences, followed by O. venulosum (51%) and C. ovina (12%). The molecular-diagnostic platform established can be used for species- or genus-specific diagnosis of patent nematode infections within 24h (compared with 7-10 days for LC), and is a sensitive and cost effective tool for routine application in research and service laboratories.
Characterization of the Ca2+-Gated and Voltage-Dependent K+-Channel Slo-1 of Nematodes and Its Interaction with Emodepside
Publisher: Public Library of Science (PLoS)
Date: 18-12-2014
Genetic characterization of selected parasites from people with histories of gastrointestinal disorders using a mutation scanning-coupled approach
Publisher: Wiley
Date: 26-05-2013
Abstract: A SSCP analysis and targeted sequencing approach was used for the genetic characterization of some major pathogens from a cohort of 227 people with histories of gastrointestinal disorders. Genomic DNAs from fecal s les were subjected to PCR- lification of regions in the glycoprotein (gp60) or triose phosphate isomerase (tpi) gene, or the second internal transcribed spacer of nuclear ribosomal DNA (ITS-2). Cryptosporidium, Giardia, and strongylid nematodes were detected in 94, 132 and 12 s les. Cryptosporidium hominis subgenotypes IbA10G2, IdA15G1, IgA17, IgA18, and IfA13G1 were identified in 74.6, 16.9, 5.6, 1.4, and 1.4% of 71 s les, respectively. For Cryptosporidium parvum, subgenotypes IIaA17G2R1 (47.6%) and IIaA18G3R1 (23.8%) were identified in 23 s les. Giardia duodenalis assemblage B (78%) was more common than assemblage A (22%). In addition, DNA of the nematodes Ancylostoma ceylanicum (n = 2), Ancylostoma duodenale (4), Necator americanus (5), and Haemonchus contortus (1) was specifically detected. This is the first report of A. ceylanicum in two persons in Australia and, we provide molecular evidence of H. contortus in a child. This SSCP-based approach should provide a useful diagnostic and analytical tool for a wide range of pathogens.
Progress on the transcriptomics of carcinogenic liver flukes of humans-Unique biological and biotechnological prospects
Publisher: Elsevier BV
Date: 11-2010
DOI: 10.1016/J.BIOTECHADV.2010.07.006
Abstract: Liver flukes, such as Clonorchis sinensis and Opisthorchis viverrini, are food-borne parasites that have a major impact on the health of humans and animals, particularly in Asia. However, the impact of C. sinensis and O. viverrini, in particular, is exacerbated in that these parasites can induce a malignant, untreatable cancer (cholangiocarcinoma, CCA) in chronically infected people. As a result, these flukes are classified as Group 1 carcinogens. Despite their substantial socio-economic importance, little is known about these parasites and their relationship with the definitive hosts at the molecular level. Here, we provide a background on these two carcinogenic flukes and review recent progress on characterizing their transcriptomes using next-generation technologies. We also describe the prospects that the transcriptomes of C. sinensis and O. viverrini provide as a resource for future -omic explorations and efforts to develop improved methods of intervention and control against these important pathogens and CCA, leading to biotechnological outcomes.
Zoonotic Ancylostomiasis: An Update of a Continually Neglected Zoonosis.
Publisher: American Society of Tropical Medicine and Hygiene
Date: 08-07-2020
Techniques for the Diagnosis of Fasciola Infections in Animals
Publisher: Elsevier
Date: 2014
Barcoding of Giardia duodenalis isolates and derived lines from an established cryobank by a mutation scanning-based approach
Publisher: Wiley
Date: 08-2011
Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut
Publisher: Cold Spring Harbor Laboratory
Date: 05-04-2022
DOI: 10.1101/2022.04.05.487115
Abstract: Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory vector mosquito provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development in the mosquito gut, from unfertilized female gametes through the first 20 hours post blood feeding, including the zygote and ookinete stages. This study revealed the transcriptional trajectories of the ApiAP2 family of transcription factors, and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structure-based functional predictions we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody or peptide-based transmission suppression strategies.
Hierarchical modelling of immunoglobulin coated bacteria in dogs with chronic enteropathy shows reduction in coating with disease remission but marked inter-individual and treatment-response variability
Publisher: Public Library of Science (PLoS)
Date: 19-08-2021
DOI: 10.1371/JOURNAL.PONE.0255012
Abstract: Chronic enteropathies are a common problem in dogs, but many aspects of the pathogenesis remain unknown, making the therapeutic approach challenging in some cases. Environmental factors are intimately related to the development and perpetuation of gastrointestinal disease and the gut microbiome has been identified as a contributing factor. Previous studies have identified dysbiosis and reduced bacterial ersity in the gastrointestinal microbiota of dogs with chronic enteropathies. In this case-controlled study, we use flow cytometry and 16S rRNA sequencing to characterise bacteria highly coated with IgA or IgG in faecal s les from dogs with chronic enteropathy and evaluated their correlation with disease and resolution of the clinical signs. IgA and IgG-coated faecal bacterial counts were significantly higher during active disease compared to healthy dogs and decreased with the resolution of the clinical signs. Characterisation of taxa-specific coating of the intestinal microbiota with IgA and IgG showed marked variation between dogs and disease states, and different patterns of immunoglobulin enrichment were observed in dogs with chronic enteropathy, particularly for Erysipelotrichaceae , Clostridicaceae , Enterobacteriaceae , Prevotellaceae and Bacteroidaceae , families. Although, members of these bacterial groups have been associated with strong immunogenic properties and could potentially constitute important biomarkers of disease, their significance and role need to be further investigated.
Differences in transcription between free-living and CO2-activated third-stage larvae of Haemonchus contortus
Publisher: Springer Science and Business Media LLC
Date: 27-04-2010
Abstract: The disease caused by Haemonchus contortus , a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a cuticle (sheath) and, once ingested with herbage by the host, undergoes an exsheathment process that marks the transition from the free-living (L3) to the parasitic (xL3) stage. This study explored changes in gene transcription associated with this transition and predicted, based on comparative analysis, functional roles for key transcripts in the metabolic pathways linked to larval development. Totals of 101,305 (L3) and 105,553 (xL3) expressed sequence tags (ESTs) were determined using 454 sequencing technology, and then assembled and annotated the most abundant transcripts encoded transthyretin-like, calcium-binding EF-hand, NAD(P)-binding and nucleotide-binding proteins as well as homologues of Ancylostoma -secreted proteins (ASPs). Using an in silico -subtractive analysis, 560 and 685 sequences were shown to be uniquely represented in the L3 and xL3 stages, respectively the transcripts encoded ribosomal proteins, collagens and elongation factors (in L3), and mainly peptidases and other enzymes of amino acid catabolism (in xL3). Caenorhabditis elegans orthologues of transcripts that were uniquely transcribed in each L3 and xL3 were predicted to interact with a total of 535 other genes, all of which were involved in embryonic development. The present study indicated that some key transcriptional alterations taking place during the transition from the L3 to the xL3 stage of H. contortus involve genes predicted to be linked to the development of neuronal tissue (L3 and xL3), formation of the cuticle (L3) and digestion of host haemoglobin (xL3). Future efforts using next-generation sequencing and bioinformatic technologies should provide the efficiency and depth of coverage required for the determination of the complete transcriptomes of different developmental stages and/or tissues of H. contortus as well as the genome of this important parasitic nematode. Such advances should lead to a significantly improved understanding of the molecular biology of H. contortus and, from an applied perspective, to novel methods of intervention.
Molecular evidence for a cryptic species within the parasitic nematode Macroponema comani (Strongyloidea: Cloacininae)
Publisher: Elsevier BV
Date: 08-2012
DOI: 10.1016/J.MCP.2012.03.002
Abstract: Nematodes resembling Macroponema comani, a common parasite of eastern grey kangaroos, Macropus giganteus, in eastern Australia were collected from an unexpected host species, the northern wallaroo, Macropus robustus woodwardi, in the Northern Territory, representing a highly disjunct occurrence. Although these specimens showed no morphological differences when compared with Ma. comani from M. giganteus, sequencing of the first and second internal transcribed spacers ITS-1 and ITS-2 of the nuclear ribosomal DNA revealed seven base pair differences in each spacer region between the two taxa. These differences included a number of autapomorphies. Sequences from both taxa differed significantly from those of Ma. beveridgei, a common parasite of the common wallaroo, Macropus robustus robustus and the euro, M. robustus erubescens. Based on these findings, the specimens in M. r. woodwardi are considered to represent a crypic species.
Genetic richness and diversity in Cryptosporidium hominis and C. parvum reveals major knowledge gaps and a need for the application of “next generation” technologies — Research review
Publisher: Elsevier BV
Date: 2010
DOI: 10.1016/J.BIOTECHADV.2009.08.003
Abstract: Cryptosporidium species (apicomplexan protists) are a major cause of diarrhoeal disease (= cryptosporidiosis) in humans worldwide. The impact of cryptosporidiosis is also compounded by the spread of HIV/AIDS and a lack of cost-effective anti-cryptosporidial chemotherapeutics or vaccines. Mitigation of the impact of cryptosporidiosis in humans needs to focus on prevention and control strategies, built on a sound understanding of the epidemiology of Cryptosporidium species. Refined epidemiological studies rely on the use of molecular tools employing informative genetic markers. Currently, the 60-kDa glycoprotein gene (gp60) is the most suitable and widely used genetic marker for Cryptosporidium species infecting humans. Here, we undertake an analysis of all publicly-available gp60 sequence data and associated literature for C. hominis and C. parvum, and yield useful insights into the richness, ersity and distribution of genetic variants, and link these variants to human cryptosporidiosis. This global analysis reveals that, despite high genetic richness in Cryptosporidium isolates from humans, there is a surprisingly low ersity. It also highlights limited knowledge about the genetics of cryptosporidiosis in developing nations and in many animals that might act as infection sources. Clearly, there is a major need for more comprehensive studies of Cryptosporidium infecting humans and other animals in Africa and Asia. As molecular technologies improve and become affordable, future studies should utilize "next generation" sequencing and bioinformatic platforms to conduct comparative 'genome sequence surveys' to test the validity of current genetic classifications based on gp60 data. Complemented by in vitro and in vivo investigations, these biotechnological advances will also assist significantly in the search for new intervention strategies against human cryptosporidiosis.
In vitro selection of Giardia duodenalis for Albendazole resistance identifies a β-tubulin mutation at amino acid E198K
Publisher: Elsevier BV
Date: 08-2021
Transcriptome and histone epigenome of Plasmodium vivax salivary-gland sporozoites point to tight regulatory control and mechanisms for liver-stage differentiation in relapsing malaria
Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.IJPARA.2019.02.007
Abstract: Plasmodium vivax is the key obstacle to malaria elimination in Asia and Latin America, largely attributed to its ability to form resilient hypnozoites (sleeper cells) in the host liver that escape treatment and cause relapsing infections. The decision to form hypnozoites is made early in the liver infection and may already be set in sporozoites prior to invasion. To better understand these early stages of infection, we undertook a comprehensive transcriptomic and histone epigenetic characterization of P. vivax sporozoites. Through comparisons with recently published proteomic data for the P. vivax sporozoite, our study found that although highly transcribed, transcripts associated with functions needed for early infection of the vertebrate host are not detectable as proteins and may be regulated through translational repression. We identified differential transcription between the sporozoite and published transcriptomes of asexual blood stages and mixed versus hypnozoite-enriched liver stages. These comparisons point to multiple layers of transcriptional, post-transcriptional and post-translational control that appear active in sporozoites and to a lesser extent hypnozoites, but are largely absent in replicating liver schizonts or mixed blood stages. We also characterised histone epigenetic modifications in the P. vivax sporozoite and explored their role in regulating transcription. Collectively, these data support the hypothesis that the sporozoite is a tightly programmed stage to infect the human host and identify mechanisms for hypnozoite formation that may be further explored in liver stage models.
An improved method for PCR-based detection and routine monitoring of geosmin-producing cyanobacterial blooms
Publisher: Elsevier BV
Date: 06-2018
DOI: 10.1016/J.WATRES.2018.02.041
Abstract: Production of taste and odour (T/O) compounds, principally geosmin, by complex cyanobacterial blooms is a major water quality issue globally. Control of these cyanobacteria imposes a significant cost on water producing and dependent industries, and requires routine monitoring and management. Classic monitoring methods, including microscopy and direct chemical analysis, lack sensitivity, are laborious, expensive or cannot reliably identify the source of geosmin production. Polymerase Chain Reaction (PCR) based tools targeting the geosmin synthase gene (geoA) provide a novel tool for routine monitoring. However, geoA is variable at the nucleotide level and potential geosmin producers represent a broad taxonomic distribution, such that multiple PCR primers with distinct lification protocols are needed to target all potential sources of this important T/O compound. Development of novel primers is hindered by a lack of sequence data and limited field and laboratory data on geosmin producers prevents prioritizing taxa for PCR testing. Here we performed a genetic screen of 253 bloom s les from Victoria, Australia using each existing PCR protocol targeting geoA. We detected Dolichospermum ucrainicum as the major geosmin producer (87% of sequenced s les) along with 3 unknown geoA sequence types. Using these data, we designed a novel, short licon, PCR protocol utilising a single standardised primer pair, capable of lifying all geoA positive s les in our study, as well as a Nostoc punctiforme positive control. This single protocol geoA PCR can further be tested on other geosmin producers and will simplify routine monitoring of T/O producing cyanobacteria.
The importance of host ecology in thelastomatoid (Nematoda: Oxyurida) host specificity
Publisher: Elsevier BV
Date: 09-2006
DOI: 10.1016/J.PARINT.2006.03.001
Abstract: An experimental investigation of host specificity within the Thelastomatoidea is presented by means of a comparison of the thelastomatoids of two panesthiine cockroaches, Panesthia cribrata and P. tryoni tryoni, with those of other log-dwelling arthropods and those of leaf litter dwelling arthropods found near by. 145 log-dwelling and leaf-litter dwelling arthropods, representing adjacent ecological niches, were collected from Lamington National Park, Queensland, Australia. A high degree of thelastomatoid species sharing (19 incidences from 26 specimens) occurs between log-dwelling arthropods and the two cockroach species. No overlap in thelastomatoid fauna was observed between the log dwelling and leaf-litter dwelling groups. Our results suggest that host specificity of thelastomatoids is largely dictated by host ecology.
A practical and cost-effective mutation scanning-based approach for investigating genetic variation in Cryptosporidium
Publisher: Wiley
Date: 11-2007
Abstract: In the present study, we used a mutation scanning-targeted sequencing approach to assess variation in part (pgp60) of the 60 kDa glycoprotein (gp60) gene among Cryptosporidium s les from humans in Victoria, Australia. Two nuclear ribosomal loci (the small subunit rRNA gene and the second internal transcribed spacer) were used to identify the s les as Cryptosporidium hominis (n = 74), Cryptosporidium parvum (n = 23) or Cryptosporidium meleagridis (n = 1). In total, nine distinct pgp60 sequences were identified (three C. hominis, five C. parvum and one C. meleagridis). Phylogenetic analyses of the pgp60 sequence data, employing well-defined reference sequences for comparison, allowed the genotypic and subgenotypic classification of s les. The C. hominis s les were classified as Ib A10G2R2, Id A15G1R2, and a new genotype, designated Ib2, was identified subgenotypically as A18G1R4. The C. parvum s les were classified as IIa A18G3R1, IIa A20G3R1, IIa A22G3R1, IIa A23G3R1 and IIc A5G3R2. These findings suggested that the C. hominis metapopulation is largely homogeneous, consisting of a single dominant genotype, Ib A10G2R2, whereas the C. parvum metapopulation is considerably more heterogeneous, with no single dominant genotype. The greater level of genetic heterogeneity found among the C. parvum s les, despite the smaller s le size, may relate to the zoonotic infection pattern of this species, which would be reflective of a greater number of possible infection sources. The present mutation scanning approach, coupled with targeted sequencing of genetically distinct representatives, is a practical, cost-effective tool for large-scale population genetic and epidemiological studies of Cryptosporidium and other eukaryotic organisms.
Analysis of nucleotide variation within the triose-phosphate isomerase gene of Giardia duodenalis from sheep and its zoonotic implications
Publisher: Wiley
Date: 2010
Abstract: This study explored the genetic composition of Giardia in fecal s les from 284 in idual lambs on pasture-based sheep farms in three regions of Victoria, Australia. An approach, combining targeted sequencing, phylogenetic analysis and PCR-coupled restriction endonuclease fingerprinting, was used to identify and genetically categorize Giardia present in 43 (15.1%) of the 284 s les and to infer their zoonotic potential. The specific identity and genetic classification were based on the phylogenetic analysis of sequence data for a portion of the triose-phosphate isomerase gene. Fourteen different sequence variants (including seven sequences that contained between one and five polymorphic sites) representing two distinct assemblages of Giardia (recognized in the current literature) were defined, of which 13 were new records. One dominant sequence type (with accession no. GQ444447, representing a genotype within assemblage A) has been detected previously in humans and is thus considered to be of zoonotic potential. (Nucleotide sequences reported in this article are available in the GenBank database under accession nos. GQ444447-GQ444451 and GQ444454-GQ444462).
Getting the most out of parasitic helminth transcriptomes using HelmDB: Implications for biology and biotechnology
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.BIOTECHADV.2012.12.004
Abstract: Compounded by a massive global food shortage, many parasitic diseases have a devastating, long-term impact on animal and human health and welfare worldwide. Parasitic helminths (worms) affect the health of billions of animals. Unlocking the systems biology of these neglected pathogens will underpin the design of new and improved interventions against them. Currently, the functional annotation of genomic and transcriptomic sequence data for socio-economically important parasitic worms relies almost exclusively on comparative bioinformatic analyses using model organism- and other databases. However, many genes and gene products of parasitic helminths (often >50%) cannot be annotated using this approach, because they are specific to parasites and/or do not have identifiable homologs in other organisms for which sequence data are available. This inability to fully annotate transcriptomes and predicted proteomes is a major challenge and constrains our understanding of the biology of parasites, interactions with their hosts and of parasitism and the pathogenesis of disease on a molecular level. In the present article, we compiled transcriptomic data sets of key, socioeconomically important parasitic helminths, and constructed and validated a curated database, called HelmDB (www.helmdb.org). We demonstrate how this database can be used effectively for the improvement of functional annotation by employing data integration and clustering. Importantly, HelmDB provides a practical and user-friendly toolkit for sequence browsing and comparative analyses among ergent helminth groups (including nematodes and trematodes), and should be readily adaptable and applicable to a wide range of other organisms. This web-based, integrative database should assist 'systems biology' studies of parasitic helminths, and the discovery and prioritization of novel drug and vaccine targets. This focus provides a pathway toward developing new and improved approaches for the treatment and control of parasitic diseases, with the potential for important biotechnological outcomes.
Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets
Publisher: Frontiers Media SA
Date: 25-08-2022
DOI: 10.3389/FCIMB.2022.986314
Abstract: The resilience of Plasmodium vivax , the most widely-distributed malaria-causing parasite in humans, is attributed to its ability to produce dormant liver forms known as hypnozoites, which can activate weeks, months, or even years after an initial mosquito bite. The factors underlying hypnozoite formation and activation are poorly understood, as is the parasite’s influence on the host hepatocyte. Here, we shed light on transcriptome-wide signatures of both the parasite and the infected host cell by sequencing over 1,000 P. vivax -infected hepatocytes at single-cell resolution. We distinguish between replicating schizonts and hypnozoites at the transcriptional level, identifying key differences in transcripts encoding for RNA-binding proteins associated with cell fate. In infected hepatocytes, we show that genes associated with energy metabolism and antioxidant stress response are upregulated, and those involved in the host immune response downregulated, suggesting both schizonts and hypnozoites alter the host intracellular environment. The transcriptional markers in schizonts, hypnozoites, and infected hepatocytes revealed here pinpoint potential factors underlying dormancy and can inform therapeutic targets against P. vivax liver-stage infection.
DETERMinants of quality of life, care and costs, and consequences of INequalities in people with Dementia and their carers (DETERMIND): A protocol paper.
Publisher: Wiley
Date: 25-12-2019
DOI: 10.1002/GPS.5246
Abstract: DETERMIND (DETERMinants of quality of life, care and costs, and consequences of INequalities in people with Dementia and their carers) is designed to address fundamental, and, as yet unanswered questions about inequalities, outcomes and costs following diagnosis with dementia. These answers are needed to improve the quality of care and equity of access to care, and therefore the quality of life, of people with dementia and their carers. DETERMIND is a programme of research consisting of seven complementary workstreams (WS) exploring various components that may result in unequal dementia care: WS1: Recruitment and follow-up of the DETERMIND cohort-900 people with dementia and their carers from three geographically and socially erse sites within six months following diagnosis, and follow them up for three years. WS2: Investigation of the extent of inequalities in access to dementia care. WS3: Relationship between use and costs of services and outcomes. WS4: Experiences of self-funders of care. WS5: Decision-making processes for people with dementia and carers. WS6: Effect of diagnostic stage and services on outcomes. WS7: Theory of Change informed strategy and actions for applying the research findings. During the life of the programme, analysing baseline results and then follow-up of the DETERMIND cohort over 3 years, we will establish evidence on current services and practice. DETERMIND will deliver novel, detailed data on inequalities in dementia care and what drives positive and negative outcomes and costs for people with dementia and carers, and identify factors that help or hinder living well with dementia.
Genetic variation within the Hypodontus macropi (Nematoda: Strongyloidea) complex from macropodid marsupial hosts in Australia
Publisher: Wiley
Date: 12-2012
Abstract: Genetic variation was investigated in the strongylid nematode Hypodontus macropi from macropodid marsupials using the second internal transcribed spacer of ribosomal DNA. A total of 547 specimens from ten species of hosts, representing all of the known hosts of the parasite, from across the Australian continent was examined. Phylogenetic analyses revealed distinct genetic clades in each of Macropus agilis, M. dorsalis, M. rufogriseus, M. bicolor, Petrogale persephone, Thylogale billardierii and T. stigmatica. A further clade contained all specimens from M. robustus and M. rufus, together with two ex les of host switching by nematodes into M. fuliginosus. The latter clade was sub ided into three subclades, one comprising specimens occurring in M. robustus erubescens, M. rufus and M. fuliginosus, the second in M. r. woodwardi and the third in M. r. robustus suggesting a relationship between the subclades and the subspecies of M. robustus. The extent of the genetic differences and the fact that several of them occur in broad sympatry suggests that H. macropi as currently defined morphologically may represent as many as ten cryptic species. Limited evidence was found for co-speciation between hosts and parasites rather most relationships were better explained by host switching.
Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subte
Publisher: Cold Spring Harbor Laboratory
Date: 11-11-2021
Abstract: Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences h er annotation, experimental design, and interpretation. We have generated a new C. parvum IOWA genome assembly supported by Pacific Biosciences (PacBio) and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species: C. parvum , Cryptosporidium hominis , and Cryptosporidium tyzzeri . We made 1926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns, and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum , C. hominis , and C. tyzzeri revealed that most “missing” orthologs are found, suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation, and single-nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free, and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.
Next-Generation Molecular-Diagnostic Tools for Gastrointestinal Nematodes of Livestock, with an Emphasis on Small Ruminants
Publisher: Elsevier
Date: 2013
An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes
Publisher: Oxford University Press (OUP)
Date: 05-11-2009
DOI: 10.1093/NAR/GKP883
Sequencing and Annotation of Mitochondrial Genomes from Individual Parasitic Helminths
Publisher: Springer New York
Date: 07-10-2014
DOI: 10.1007/978-1-4939-1438-8_3
Abstract: Mitochondrial (mt) genomics has significant implications in a range of fundamental areas of parasitology, including evolution, systematics, and population genetics as well as explorations of mt biochemistry, physiology, and function. Mt genomes also provide a rich source of markers to aid molecular epidemiological and ecological studies of key parasites. However, there is still a paucity of information on mt genomes for many metazoan organisms, particularly parasitic helminths, which has often related to challenges linked to sequencing from tiny amounts of material. The advent of next-generation sequencing (NGS) technologies has paved the way for low cost, high-throughput mt genomic research, but there have been obstacles, particularly in relation to post-sequencing assembly and analyses of large datasets. In this chapter, we describe protocols for the efficient lification and sequencing of mt genomes from small portions of in idual helminths, and highlight the utility of NGS platforms to expedite mt genomics. In addition, we recommend approaches for manual or semi-automated bioinformatic annotation and analyses to overcome the bioinformatic "bottleneck" to research in this area. Taken together, these approaches have demonstrated applicability to a range of parasites and provide prospects for using complete mt genomic sequence datasets for large-scale molecular systematic and epidemiological studies. In addition, these methods have broader utility and might be readily adapted to a range of other medium-sized molecular regions (i.e., 10-100 kb), including large genomic operons, and other organellar (e.g., plastid) and viral genomes.
Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions
Publisher: Elsevier BV
Date: 03-2014
Mutation scanning-based analysis of anisakid larvae from Sillago flindersi from Bass Strait, Australia
Publisher: Wiley
Date: 27-01-2012
Abstract: Anisakidosis is an important fish-borne disease caused by the larvae of anisakid nematodes, which affects humans and a range of other animals. The accurate identification of members of this nematode group is central to investigating the epidemiology of the parasites and in the surveillance and control of anisakidosis. It is now well known that morphological identification alone does not allow specific identification, particularly of larval stages. To better understand the epidemiology of anisakid nematodes in southern Australian fishes and the potential risks posed to human health, a survey of 50 specimens of the commercially important fish, Sillago flindersi, from Bass Strait, Australia was conducted. We characterised anisakid larvae by PCR-coupled mutation scanning, sequencing and phylogenetic analyses of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA. This study revealed that 92% of the S. flindersi examined were infected with anisakids (n=194), which were represented by seven genotypes. Phylogenetic analyses of the genotypes defined herein, together with reference sequence for Anisakis pegreffii and Hysterothylacium sp. from public databases (i.e. GenBank), revealed the presence of A. pegreffii (n=24), Hysterothylacium larval type IV (n=90) and Hysterothylacium larval type VIII (n=80) in S. flindersi. Thus, the PCR-coupled mutation scanning approach employed herein is an effective tool for the genetic characterisation of anisakid nematodes for diagnostic and analytical purposes (nucleotide sequences reported in this paper are available in the GenBank database under accession nos. JN631796-809).
Classification of Cryptosporidium species from patients with sporadic cryptosporidiosis by use of sequence-based multilocus analysis following mutation scanning
Publisher: American Society for Microbiology
Date: 07-2008
DOI: 10.1128/JCM.00116-08
Abstract: In the present study, we analyzed genetic variation in Cryptosporidium species from humans ( n = 62) with clinical cryptosporidiosis in South Australia. Sequence variation was assessed in regions within the small subunit of nuclear rRNA (p-SSU), the 70-kDa heat shock protein (p- hsp70 ), and the 60-kDa glycoprotein (p- gp60 ) genes by employing single-strand conformation polymorphism analysis and sequencing. Based on the analyses of p-SSU and p- hsp70 , Cryptosporidium hominis ( n = 38) and Cryptosporidium parvum ( n = 24) were identified. The analysis of p- gp60 revealed eight distinct subgenotypes, classified as C. hominis IaA17R1 ( n = 3), IbA9G3R2 ( n = 14), IbA10G2R2 ( n = 20), and IfA12G1R1 ( n = 1), as well as C. parvum IIaA18G3R1 ( n = 15), IIaA20G3R1 ( n = 6), IIaA22G4R1 ( n = 2), and IIcA5G3R2 ( n = 1). Subgenotypes IaA17R1 and IIaA22G4R1 are new. Of the six other subgenotypes, IbA10G2R2, IIaA18G3R1, IIaA20G3R1, and IIcA5G3R2 were reported previously from the state of Victoria. This is the fourth record in Australia of C. parvum subgenotype IIaA18G3R1 from humans, which, to date, has been isolated only from cattle in other countries. This subgenotype might be a significant contributor to sporadic human cryptosporidiosis and may indicate a greater zoonotic contribution to the infection of humans in the area of study. Comparative analyses revealed, for the first time, the differences in the genetic makeup of Cryptosporidium populations between two relatively close, major metropolitan cities.
Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention
Publisher: Elsevier BV
Date: 05-2011
Recent advances in candidate-gene and whole-genome approaches to the discovery of anthelmintic resistance markers and the description of drug / receptor interactions
Publisher: Elsevier BV
Date: 12-2014
Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia
Publisher: Cold Spring Harbor Laboratory
Date: 06-04-2021
DOI: 10.1101/2021.04.06.438666
Abstract: During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the 3′ UTR of an mRNA, thus determining much of its post-transcriptional fate. Here, using long-read sequencing, we characterize the polyadenylation signal and related sequences surrounding Giardia lamblia cleavage sites for over 2600 genes. We find that G. lamblia uses a AGURAA poly(A) signal, which differs from the mammalian AAUAAA. We also describe how G. lamblia lacks common auxiliary elements found in other eukaryotes, along with the proteins that recognize them. Further, we identify 133 genes that show evidence of alternative polyadenylation. These results suggest that despite pared down cleavage and polyadenylation machinery, 3′ end formation still appears to be an important regulatory step for gene expression in G. lamblia .
New species of Cloacina von Linstow, 1898 (Nematoda: Strongyloidea) parasitic in the stomachs of wallaroos, Osphranter spp. (Marsupialia: Macropodidae) from northern Australia
Publisher: Springer Science and Business Media LLC
Date: 28-05-2018
DOI: 10.1007/S11230-018-9798-9
Abstract: Three new species of the parasitic nematode genus Cloacina von Linstow, 1898 (Strongyloidea: Cloacininae) are described from the stomachs of wallaroos, Osphranter spp. (Marsupialia: Macropodidae), from northern Australia. Cloacina spearei n. sp. is described from O. robustus woodwardi (Thomas) and O. antilopinus (Gould) and is distinguished from congeners by the shape of the cephalic papillae, the shallow buccal capsule, the presence of an oesophageal denticle and the convoluted but non-recurrent vagina in the female. Cloacina longibursata n. sp. also from O. robustus woodwardi and O. antilopinus is distinguished from congeners by the elongate dorsal lobe of the bursa, with the origin of the lateral branchlets posterior to the principal bifurcation, in the features of the spicule tip, the lack of bosses lining the oesophagus and the absence of an oesophageal denticle. Cloacina crassicaudata n. sp., from the same two host species was formerly identified as C. cornuta (Davey & Wood, 1938). Differences in the cephalic cuticle (inflation lacking in the new species), the shape of the cephalic papillae, the dorsal oesophageal tooth and the spicule tips, as well as differences in the sequences of the internal transcribed spacers of the nuclear ribosomal DNA, indicate that this is an independent species. The geographical distribution of this species is disjunct with populations in both the Northern Territory and Queensland. Possible reasons for the disjunct distribution are discussed.
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
Publisher: Springer Science and Business Media LLC
Date: 2013
First report of anatoxin-a producing cyanobacteria in Australia illustrates need to regularly up-date monitoring strategies in a shifting global distribution
Publisher: Springer Science and Business Media LLC
Date: 26-07-2019
DOI: 10.1038/S41598-019-46945-8
Abstract: Routine monitoring of toxic cyanobacteria depends on up-to-date epidemiological information about their distribution. In Australia, anatoxin producing cyanobacteria are not regularly tested for and thought to be rare if not absent from the continent. Our study investigated the presence of anatoxin-a (ATX-a) producing cyanobacteria in surface water s les (n = 226 from 67 s ling locations) collected from 2010 to 2017 across the state of Victoria, Australia. We (1) detected the presence and distribution of ana C (anatoxin-a synthetase C) gene sequences previously associated with various cyanobacteria, including Cuspidothrix issatschenkoi , Aphanizomenon sp., D. circinale, Anabaena sp., and Oscillatoria sp., from 31 s ling locations, and (2) determined the concentration of ATX-a in s les tested using ELISA, in two instances detected at µg · L −1 . These data present the first confirmation of ATX-a producers in Australia. Our study indicates that ATX-a should be included in regular testing of cyanobacterial blooms in Australia and highlights the importance of regular investigation of the distributions of toxic cyanobacteria worldwide, particularly amid the known expanding distribution of many cyanobacterial taxa in a period of increased eutrophication and rising surface water temperatures.
A theoretical study to establish the relationship between the three-dimensional structure of triose-phosphate isomerase of Giardia duodenalis and point mutations in the respective gene
Publisher: Elsevier BV
Date: 10-2010
DOI: 10.1016/J.MCP.2010.06.001
Abstract: Predicting how point mutations in genes alter the tertiary and quarternary structure of proteins is central to a number of areas of molecular biology and has implications in relation to the function and evolution of molecules. In the present study, we theoretically assessed the effects of 20 point mutations detected previously in a region of the triose-phosphate isomerase gene (tpi) of the protozoan Giardia duodenalis on the three-dimensional structure of the 'wild-type' protein (TPI). Amino acid substitutions arising from codon variations were mainly located at surface-accessible sites or in hydrophobic pockets of TPI. None of the substitutions was predicted to exert a significant change to the fold or functionality of the enzyme, with the exception of one alteration (Arg100). Almost all substitutions were either conservative or semi-conservative, and retained or even improved the expected stability of the fold. Overall, the findings provide support for the "neutral theory", which contends that evolution at the molecular level is not solely shaped by "Darwinian selection but also by random drift of selectively neutral or nearly neutral mutants".
Cryptosporidium - Biotechnological advances in the detection, diagnosis and analysis of genetic variation
Publisher: Elsevier BV
Date: 07-2008
DOI: 10.1016/J.BIOTECHADV.2008.02.003
Abstract: Cryptosporidiosis is predominantly a gastrointestinal disease of humans and other animals, caused by various species of protozoan parasites representing the genus Cryptosporidium. This disease, transmitted mainly via the faecal-oral route (in water or food), is of major socioeconomic importance worldwide. The diagnosis and genetic characterization of the different species and population variants (usually recognised as "genotypes" or "subgenotypes") of Cryptosporidium is central to the prevention, surveillance and control of cryptosporidiosis, particularly given that there is presently no broadly applicable treatment regimen for this disease. Although traditional phenotypic techniques have had major limitations in the specific diagnosis of cryptosporidiosis, there have been major advances in the development of molecular analytical and diagnostic tools. This article provides a concise account of Cryptosporidium and cryptosporidiosis, and focuses mainly on recent advances in nucleic acid-based approaches for the diagnosis of cryptosporidiosis and analysis of genetic variation within and among species of Cryptosporidium. These advances represent a significant step toward an improved understanding of the epidemiology as well as the prevention and control of cryptosporidiosis.
Diagnostic and analytical mutation scanning ofCryptosporidium: utility and advantages
Publisher: Informa UK Limited
Date: 03-2009
Abstract: Cryptosporidiosis is predominantly a disease of the alimentary tract of humans and other vertebrates, caused by parasitic protists of the genus Cryptosporidium. This disease, transmitted mainly via the fecal-oral route (in water or food), is of major socioeconomic importance globally. The diagnosis of cryptosporidiosis, including the genetic characterization of the different species, genotypes and subgenotypes (population variants) of Cryptosporidium, is crucial to prevention and control, particularly as there is no cost-effective treatment against this disease. Although traditional phenetic techniques have had major deficiencies for the specific diagnosis of cryptosporidiosis, there has been substantial progress in the establishment of molecular tools. In this article, we review key genetic markers used for the specific identification of Cryptosporidium, diagnosis of cryptosporidiosis and analysis of genetic variation in Cryptosporidium populations. We also discuss the advantages and disadvantages of selected techniques, and emphasize the benefits of utilizing rapid mutation scanning in achieving improved insights into the population genetics and epidemiology of Cryptosporidium.
Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants
Publisher: Elsevier BV
Date: 12-2013
Related Organisations
Brighton And Sussex Medical School
Location: United Kingdom of Great Britain and Northern Ireland
University Of Plymouth
Location: United Kingdom of Great Britain and Northern Ireland
Walter And Eliza Hall Institute Of Medical Research
Location: Australia
Related Funding Activities
Discovery Projects - Grant ID: DP110103175
Start Date: 01-2011
End Date: 12-2014
Amount: $420,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP180102049
Start Date: 06-2018
End Date: 12-2022
Amount: $619,046.00
Funder: Australian Research Council
View Funded ActivityLinkage - International - Grant ID: LX0882215
Start Date: 2008
End Date: 06-2011
Amount: $26,700.00
Funder: Australian Research Council
View Funded ActivityLinkage - International - Grant ID: LX0775848
Start Date: 2007
End Date: 12-2008
Amount: $84,530.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP130100209
Start Date: 03-2014
End Date: 12-2017
Amount: $599,952.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP100100091
Start Date: 09-2010
End Date: 09-2013
Amount: $240,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP160100389
Start Date: 2016
End Date: 12-2019
Amount: $336,400.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP0989137
Start Date: 05-2009
End Date: 12-2012
Amount: $830,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP120200122
Start Date: 10-2012
End Date: 12-2017
Amount: $772,500.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP130100311
Start Date: 2014
End Date: 12-2018
Amount: $612,756.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP180100835
Start Date: 02-2020
End Date: 02-2024
Amount: $456,527.00
Funder: Australian Research Council
View Funded Activity